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Nintendo Power celebrated its 20th anniversary last year, and as part of their festivities, they posted their top 20 games per Nintendo system.  Despite that they are the collected opinions of the NP staff (and I certainly don't know HOW they picked these, beyond what they stated on the first page of the feature), some of these choices really rubbed me the wrong way.  So, in the interest of discussion, I will refute some of their selections, ponder why certain games are higher than ones I feel are more deserving, and question why some great games failed to make the list.  I will not discuss every single game on their list, as it'd be hard for me to keep this engaging if I keep saying "I have no problems with this choice." :p
Naturally, you may not agree with me or with NP, and that's fine.  But I just had to get this off of my chest.  This article can be found in Issue 231, August 2008, starting on page 70.
Note - Part 1 covers the NES to the N64.  Part 2, which can be accessed here, will go from the Game Boy Advance up to the Wii.

The NES selections weren't too bad, really.  My Top 15 NES games looked somewhat like theirs.  There are a few issues I have with it, though...

1. Legend of Zelda
I can't argue with this.  The original Zelda is a fantastic game that is a joy to play, so I applaud this pick.

2. Super Mario Bros. 3

3. Mega Man 2
While I prefer MM3 over its prequel, many people do love MM2, and it's a fine game, as well.  So this isn't a bad pick by any means.

4. Super Mario Bros.

5. Metroid
Personally, I think the original Metroid has had a huge influence on gaming, but the core gameplay hasn't aged as well as some other NES titles.  Sequels Super Metroid and Metroid Zero Mission take the concepts that began here and took them to the next level.  The original feels a bit dated and clunky in comparison.  Still, it features excellent atmosphere; you do feel like you're on an alien world, and it's one of the first to capture that feeling so well.  It also was one of the earliest games that was open-ended and heavily promoted exploring.  So I can't say that NP was completely wrong in their choice; I just think some other NES games should have been higher up.

6. Punch-Out!!

7. Contra

8. Super Mario Bros. 2
I'm sorry, but SMB2 is WAY too high on this list.  Above ALL of the Castlevanias?  Mega Man 3?  Bionic Commando?  Ducktales?  In my opinion, all of these above games are much better platformers than SMB2.  It lacks the super-tight controls of its Mario cousins (probably because it's not a TRUE Mario title), and the level designs aren't quite as clever as the games I've listed above.  It's a good game, but it's not Top 10 worthy.

9. Castlevania III: Dracula's Curse

10. Ninja Gaiden
Most the gamers I know consider NG2 the peak of the franchise, but NP skipped over it completely.  NG is a great action title, but from what I recall, NG2 feels smoother and is much more refined than the original.  It's worthy of being on the list, certainly, but not in the Top 10.

11. Mega Man 3
I must give kudos to NP for including MM3; it usually gets forgotten in the Mega Man 2 fandom whirlpool.  I'm also happy that it scored so highly, because it truly is a wonderful game to play through.

12. Zelda II: The Adventure of Link
Whoa, now.  Zelda II shouldn't even be on this list.  I consider Zelda II to be one of the largest disappointments in all of gaming.  It's a landmark of how NOT to design a sequel to a best selling game.  To me, the Zelda series works best when I can observe a ton of the playfield (which both the 2D overhead and the 3D behind the back views offer), one that lets me see what's coming up and react accordingly with Link's assortment of weapons and magic.  It also gives me some repose, offering me time to think things through more clearly and to enjoy the environments I'm running around in.  Zelda II doesn't work that way.  By switching to a side scrolling format, you lose that essence of knowing what's going on.  Enemies will bombard you from the side randomly, and Link lacks many of the skills and weaponry he usually carries to fight them off.  There's also no break from enemy encounters, so the game works in a completely different fashion.  On top of that, Link's painfully short attack range, slippery controls and some mediocre level design add up to a major headache for me.  I would never consider this one of the NES greats over other titles that are much more deserving the honor.
(Note - I wrote this a while ago, and recently have been engaging in a forum discussion about Donkey Kong Jungle Beat, which also changed up many of the features of the DK franchise, alienating those who liked the characters and gameplay from DKC.  I have been arguing that DKJB is not the first Nintendo franchise to do this, and Zelda II is a poignant example.  However, I didn't want someone pointing out the potentially hypocritical statement I make in this article as evidence against my point there.  My original point at NinDB was that Nintendo has experimented with their franchises before DKJB came about, and that fans of those franchises haven't been as uptight about most of their reinventions as DKC fans are about DKJB.  Zelda II bugs me for its stark contrasts to most other Zeldas, but I think that Nintendo should play around with new ideas for their franchises.  If they didn't, we'd probably would have never gotten Super Mario 64, Zelda: Ocarina of Time or Metroid Prime, which are all fantastic games!  Having not played Jungle Beat and being fairly unimpressed with the DKC games, I may not be the best person to discuss the switches Nintendo Tokyo made to the history set by Rare's SNES titles, but I still think Zelda II did far more restructuring to the Zelda series than Jungle Beat did to Donkey Kong Country - at least it's still a platformer!)

13. Ducktales
A rare case of a licensed title being done right, Ducktales is very worthy of being on this list.

14. Castlevania

15. Castlevania II: Simon's Quest

16. Maniac Mansion

17. Bionic Commando
I'm pleased that they placed BC for the list, but why is it so low?  Bionic Commando was a fresh take on the run-n-gun, removing the ability to jump freely and replacing it with a bionic arm that requires you to think about your forward movements.  It's incredibly strategic, and it's also a gameplay treat.  The shooting action is also topnotch, and the mild RPG bits of building up a life bar and gathering gear are also well done.  An excellent game that accommodates both the platformer and shooter crowd in one fell swoop, this should have been much higher on the list than 17th.

18. Dragon Warrior IV

19. Final Fantasy
Eh.  I don't think the original FF is worthy of being on this list.  The JRPG genre has improved a lot from this early stab of helping create it, and while I don't think it's a bad game (it's quite decent, to be honest), I think other games are more deserving of being in the Top 20.

20. Kid Icarus

Some Notable Omissions:
Kirby's Adventure
I'm a bit upset that Kirby's finest platforming adventure was completely passed over.  Not only is it a very well done game with good level design, catchy music and tight controls, but it's the game that introduced Kirby's power stealing ability!  NP incorrectly lists Kirby's Dream Land 2 as its origin, but KA beat that to the punch by a few years.  A disappointing exception to the list.

Ninja Gaiden II
Another shocker.  Why was Ninja Gaiden II left out in the cold?  It refines what Ninja Gaiden did so well and nearly perfected it.  The level design was a step up, Ryu controlled better, and the graphics were among the best the NES offered.  Probably Tecmo's finest work on Nintendo's platforms, yet it was completely ignored by the NP staff.

I prefer this over Zelda II by a long shot.  Set in modern trappings (at the time of its release, anyway), Mike Jones' quest to rescue his uncle was one of the better storylines of the NES era.  A wide range of levels (island caves to tombs to volcanoes to whale stomachs to alien ships...for example), clever puzzles and a huge assortment of unique weapons (you don't see bolas and cleats as weapons every day) help make ST a very entertaining title to play.  Its controls are a little stiff, but they rarely work against you.  If you like the original Zelda, you should try this out; they are quite similar.  Shame Nintendo Power didn't, from what it seems.

Game Boy
I only have a handful of Game Boy games in my possession currently, so I may not be the best judge of this list.  I have played a few of these throughout my childhood though, so I'll pick my brain as best as I can.

1. Tetris DX
Tetris ALWAYS seems to get 1st place on the Game Boy lists that I see.  I'm not all that surprised, considering how addictive it can be.  I don't care for it, but I can understand its importance in the realm of puzzle games and the success it brought to Nintendo, so no complaints, here.  I wouldn't put it at #1, myself, though...or even on my list, to be honest.

2. Legend of Zelda: Link's Awakening DX
I would put this up at the top of the Game Boy pile.  It captures the Zelda essence very well, despite distancing itself from the usual "Princess Zelda is captured by Ganon" motif.  Great dungeons, a unique overworld and solid controls add up to a great game experience.

3. Pokemon Red/Blue
Ah, the Pokemon craze.  I did spend some time with Red, and while I thought the game was adequate for what it does, I don't know if I'd have it this high up.  I think there's a few other GB games that are better at what they do than the first stab at "Gotta Catch Em All!"  Although, this feeling might have something to do with the fact that I couldn't get a Meowth in Red...

4. Legend of Zelda: Oracle of Seasons

5. Legend of Zelda: Oracle of Ages
Ages isn't quite as good as Link's Awakening, but I'd probably have it up this high as well.  Capcom did well with their initial Zeldas, so I think this is a fitting place for it.  

6. Pokemon Gold/Silver

7. Super Mario Land 2: Six Golden Coins

8. Donkey Kong
This is such a great game.  It combines the platforming of Mario, the arcade action of the original DK and brain-teasing puzzles into an enjoyable blend of genres.  The key component is Mario's quick responsiveness to your commands.  If the controls weren't so tight, the gameplay would fall flat on its face (a la Mario Vs. Donkey Kong, which tried to replicate the feeling of this title, but failed miserably at it).  I'd consider this the 2nd best GB title I've played, so 8th isn't too far off from where I'd put it, I guess.

9. Wario Land 3

10. Kirby's Dream Land 2

11. Metal Gear Solid

12. Metroid II: Return of Samus

13. Pokemon Puzzle Challenge

14. Mega Man V

15. Teenage Mutant Ninja Turtles: Fall of the Foot Clan
Putting this on the list is an odd choice; perhaps NP felt a little guilty about not including the two better beat-em-ups for the NES.  It's kind of like the original TMNT title on the NES, only it's more relevant to the series, and it's a lot easier.  That being said, it's a standard action game that brought little to the table in terms of innovations or gameplay ideas, so I don't understand the reasoning behind picking this over some other GB games that deserve more Kid Icarus: Of Myths & Monsters, for example.

16. Mario's Picross

17. Dr. Mario

18. Kid Icarus: Of Myths and Monsters
The second take of KI is a much more balanced game than its NES prequel.  The game scrolls down as well as up, reducing the frustrations of platforming.  I haven't beaten it, but it does feel better than the original, and it does offer up a nice challenge without feeling quite so cheap.  I'd put this up higher from my brief playtime than here, myself.

19. Shantae

20. Operation C

Some Notable Omissions:
None I can think of at the moment.  Like I said, my experience with the Game Boy is not as through as others.

Super NES
I have only recently been collecting SNES games, and haven't played all of the titles I've acquired yet.  So I may again be a bit limited in my responses.

1. Legend of Zelda: Link to the Past
I've mentioned this before, but Link to the Past, while certainly an excellent game, is not my favorite Zelda.  It is worthy, however, of being considered the finest SNES game.  I'd put a few above it (as I do on my own list), but it's a respectable choice.

2. Super Mario World
On the contrary, I do not think that SMW is deserving of a #2 spot on this list.  It's a fun platformer, for sure, but is it THAT great to get the second spot on the list?  No.  There's a bunch of much better candidates that deserve this ranking more than SMW.

3. Final Fantasy III

4. Super Metroid
I'm not surprised that Super Metroid is this high.  It's a fantastic game rich with atmosphere, packed with secrets and features the finest 2D gameplay experience I've ever played.  I have no qualms here, outside of wanting to place it even higher, of course.

5. Chrono Trigger
Chrono Trigger was a dream team of RPG developers; a merger of Square and Enix's finest talent BEFORE they actually united later on.  With one of the best soundtracks in gaming, a very solid plot line, an engaging battle system and a bevy of endings to uncover, CT is very worthy of this position.

6. Street Fighter II: Turbo
Hm.  For Nintendo systems, I can't really debate this choice.  Street Fighter II Turbo is by some people's measure the best in the series, and considering that Capcom has slighted the N64 and Gamecube from many of its sequels (Capcom Vs. SNK 2 EO does not count, although that is one excellent fighter!), this isn't a bad pick to represent Street Fighter.  I don't know if I'd put it this high, myself, though.

7. Contra III: The Alien Wars

8. Super Mario World 2: Yoshi's Island

9. Super Mario Kart
A lot of people seem to think that this remains the golden title in the Mario Kart series.  Nintendo Power clearly doesn't (and I'll get to the sequels down the road).  They still plopped the original kart-racer in the top 10 though, so I must say my piece here, too.  I think ALL of the Mario Kart games that I've played (Double Dash notwithstanding) are worthy of being on their respective lists, but not up in the top 10.  They're fun, especially with friends, but I just can't say that they're SO good that they beat out a bunch of other games that I got a bigger thrill out of.

10. Super Castlevania IV

11. Mega Man X
I just can NOT get into the MMX games.  I try and I try, but they bore me.  Something isn't clicking on the delightful old-school MM vibe with me, and I just don't want to make the effort into playing them.  I believe that the switch into the Charge shot is a major factor; it makes the game more of a blast-off than a twitch shooter, which I think I prefer.  MM2 and MM3 will do it for me, I think.

12. Actraiser

13. TMNT IV: Turtles in Time

14. Super Punch-Out!!

15. Secret of Mana
A great game stuck way too far down on their list.  The high point of the series (outside of import-only Seiken Densetsu 3), this action-RPG has tight controls, a multiplayer mode that is tremendous, and has some of the most appealing graphics and music for the system.   

16. Final Fantasy II

17. F-Zero

18. Axelay

19. Earthworm Jim

20. Pilotwings
Pilotwings?  PILOTWINGS?!?  Above the omissions I've listed below?  Wow.  Pilotwings was a neat game at its launch, I'm sure, but it's quite dated nowadays.  I didn't think it was all that impressive when I tried it out a while ago.  It did not control all that well, which makes the precision they demand all the more irritating.  But man, I'm just blown away that NP skipped over the fan-favorite Earthbound, the excellent Kirby Super Star, and the solid Super Mario RPG for this antiquated launch title.

Some Notable Omissions:
Earthbound is a quirky RPG with tons of character and personality.  Ness has been a prominent star of the Smash Bros. series, popping up in all three titles.  Catchy music, trippy visuals and some of the most unique enemies in existence...why skip over this gold mine of RPG fun, NP?

Kirby Super Star
Outside of Kirby's Adventure, this is the finest platformer Sakurai's creation has popped up in.  Tons of gameplay await you here, with 9 different modes of play and some of the best platforming in the series to date.  Alas, this was also passed up.

Super Mario RPG
Lastly, NP declined Square's final RPG for the Super NES, which is very weird.  Square set into motion the unique gameplay of future Mario RPG's (all of which ARE included on their respective system lists), namely the action commands.  It also enriched the Mushroom Kingdom with its inclusion of many new realms, a concept that future Mario's would continue to implement.  It's not my favorite of the Mario RPG bunch, but it's still a fine game, and is quite worthy of being on the list.  Why it isn't...and Pilotwings a mystery for the ages.

Heh, now is when things begin to start getting loony.  It wasn't until I read this particular bit of their feature that I really felt the need to argue about their decisions.  There's many gems missing off of this list, and there are some questionable choices all the way through.

1. Legend of Zelda: Ocarina of Time
This is my 2nd favorite game of all time, so I certainly have no arguments here...

2. Super Mario 64
...and this is 5th on my list, so I won't question this choice, either.

3. Mario Kart 64
I CAN, however, argue about this one.  I feel that this is the best Mario Kart game I've played; the tracks are fairly fun (and not too crazy, like the later games tended to push), the Blue Shell wasn't as cheap as it became later on, and the multiplayer mode is one of the greatest on the system.  But to say that it's the third best N64 game of all time?  That's just not right.  I've played most of the games on this list, and I would consider a large chunk of them to be better overall experiences to Mario Kart 64.  I had this on my personal favorite N64 game list, but it was significantly lower than 3rd place, where I think it belongs.  3rd place is a bit insulting to the heaps of better games below it.

4. Goldeneye 007
Goldeneye is such a landmark game.  Probably Rare's finest hour, they nailed a new frontier for FPS'es to head into, packed in one of the best multiplayer experiences before the online realm took off, and the game featured tight controls and solid level design.  This is how you tackle a license.  This deserves to be this high, no question.

5. Star Fox 64
I like Star Fox 64, don't get me wrong.  It's a competent shooter, with tight gameplay, tricky boss fights and branching levels.  The multiplayer mode was brainless, but the single-player game was a lot of fun.  It's one of the few shooters of this variety I do enjoy (granted, I haven't played many of them).  But is it the 5th greatest N64 game on that one merit alone?  Nope.  When I look at Paper Mario, Ogre Battle 64, Zelda: Majora's Mask, Wave Race 64, and my grand list of games Nintendo Power did not plop on their list below, Star Fox 64 comes up short.  They are much better games than SF64 on the whole.

6. Legend of Zelda: Majora's Mask
Easily the most bizarre Zelda in existence, Majora's Mask decided to forego many of the usual conventions of the series.  Its use of time-travel as its major gameplay mechanic was very clever, letting Link tackle a particular challenge throughout the game's three days before the moon crashed.  The controls were as smooth as OoT, and the inclusion of masks that changed Link into one of the three other dominant races in Termina was a cool idea.  Alas, the game suffered from a meager dungeon lineup; only 5 appeared in the game in total, a staggering drop from any Zelda that preceded it.  Thankfully, they were all excellently designed, making the loss a little more bearable.  The addition of a Happy Notebook was an interesting decision, one that made Link's quest feel more personal than it had before.  It's a bit of a shame that those characters forget what you've done for them when you slip back in time, but I still think the realm of Termina is the series' most intimate, even with Wind Waker and Twilight Princess added to the equation.  Some may consider the constant looping of the three days a bit dull, and that is a valid argument, but I don't think this is a bad place for Majora's Mask.  It is very different than the usual Zelda titles, but in this case (unlike Zelda II), it's a very delightful game, and I can understand it being in the top 10.

7. WWF No Mercy

8. Jet Force Gemini
Did NP play a different Jet Force Gemini than me?  I thought JGF was a fantastic 3D action title for the first chunk of the game.  But, once you beat the "final" boss and the game suddenly required copious backtracking of already-explored planets to find one room that only your current character can reach, only to have to repeat the whole level with the other two to reach two other got really old really fast.  It's a shame that Rare felt the need to tack on those extra bits to lengthen the game, because I was having a really good time until that happened.  Backtracking must be done really carefully to not become tedious.  Metroid has mastered it, and Rare should have studied up a bit more on RD1's work before trying it themselves.  If I were to consider JFG's excellent beginning alone, I could make a strong argument for it being in the Top 20.  But the whole dragged-out experience?  Nah.

9. Wave Race 64
This is a great racing game.  I am not a huge fan of them, but Nintendo really nailed the experience of the sport's random conditions thanks in part to the realistic oceanic waves that the racers must battle on top of their competition.  Each race is different because of it, and the courses are also well thought out, offering shortcuts that vary due to the water's chaos.  Nintendo's racing lineup was excellent on the N64, and this may be the best of the bunch.  A fine choice.

10. Conker's Bad Fur Day

11. F-Zero X
My copy of F-Zero X locked up after a few tracks, so I can only comment about the early parts of the game.  The sense of speed was incredible.  I think it feels faster than any other racing game I've touched.  Even F-Zero GX and its gorgeous tracks feel a touch slower than this.  The sparse environments didn't hurt the frantic pace, and on the whole I can understand the reasoning behind this pick.  I don't have it on my list, but I haven't played it enough to have much more of an opinion than this.

12. Star Wars: Rogue Squadron
Rogue Squadron is probably the best Star Wars title on a Nintendo system.  It captured the essence of space combat very well, and it looked amazing for a N64 game.  I don't tend to like games like this, so I wouldn't put it on my list, myself.  But from what little I played of it, it felt solid enough for me to see why people would include it on a list like this.

13. Paper Mario

14. Ogre Battle 64: Person of Lordly Caliber
Yay!  The N64's finest RPG is very worthy of being on this list, and the top 15 isn't shabby, either.  I'd have it higher, naturally, but at least they acknowledged it!

15. Super Smash Bros.
I liked SSB back in the day, but I really do feel that both Melee and Brawl have rendered it obsolete.  That said, I wouldn't plop it onto a N64 list either, because there's a vast quantity of other games that I think are much better.

16. Rayman 2: The Great Escape

17. Mario Golf
Ah, Mario Golf.  Once again, I must smite thee.  I can not stand Mario Golf's character ratings.  It drives me batty.  I want Luigi to be able to golf with Mario and not have to fight an uphill battle, you know?  I really do prefer Mario Golf: Toadstool Tour to this on about every level, and fail to understand what appeal the N64 prequel has compared to it.

18. Rocket: Robot on Wheels

19. Pokemon Snap
Snap was quaint, certainly, but as a gameplay exercise, it is fairly basic and nowhere near the most compelling or engaging of the N64's lineup.  Snapping pictures of Meowth does not beat out battling bots in Perfect Dark, landing tough tricks in 1080, or blasting aliens from a motorcycle in Body my humble opinion, of course.  So no, it shouldn't be on the list.

20. Blast Corps
Rare's destruction game is worthy of being on a Top 20 list, methinks.  The replay is a bit limited, but the initial runthrough is a blast (literally).

Some Notable Omissions:
Body Harvest
I love Body Harvest.  It's one of the finest 3D action games I've played, with plenty of tension, a fairly wide selection of vehicles to pick from, mostly adequate controls, and it manages to throw the right amount of chaos at you.  Considering that GTA3 ran with many of the same gameplay concepts Body Harvest presented, it's a very worthy game to try out.  Really wish it got some recognition.

Perfect Dark
I'm a bit surprised that NP skipped Perfect Dark.  I personally think that Rare defined the N64's multiplayer abilities with PD, taking the core that Goldeneye spectacularly achieved and polishing it to near-perfection.  Sure, there's slowdown and some dud weapons, but on the whole PD's multiplayer alone is enough for me to consider it Top 20 worthy.  Single player manages to be mostly fun, too, but it begins to drag a bit towards the end.  In the end, PD is great fun, and I'm sad it was not represented.

1080 Snowboarding
I've played Avalanche, I've played SSX3, but I still consider 1080's N64 debut the pinnacle of snowboarding games.  The tight controls and precision tricks required made this like a fighting game to me, which I greatly relished.  The excellent graphics (near the top the system ever put out, in my opinion) helped make the game all the more real, as well.  One of the finest sports games of all time, easily, yet was snubbed on this list.

International Superstar Soccer 98
Konami's soccer series is also one of the finest sports games of all time, one that really nailed the team concept.  The AI is aggressive, the controls are excellent, and the atmosphere was amazing for its time.  Stuffing 22 polygonal players onto one pitch was a lot to ask of the N64, but the game rose to the challenge, only sputtering during some of the celebration clips.  Simply a fun game to play.

Another Rare title that surprised me with its absence, Banjo-Kazooie took Mario 64's basic elements and tweaked them around to make another fine 3D platformer.  It didn't push the boundaries (outside of its amazing visuals for the system), but it didn't need to.  It controls well, has great music, some clever level designs (despite running with the usual platformer level varieties), and had some punishing gameplay moments that were very satisfying to complete.  Why it isn't on the list is dumbfounding to me.

Resident Evil 2
Lastly, Angel Studios' (now Rockstar San Diego) remarkable port of Resident Evil 2 failed to get on the list.  I think that RE2 is the best of the original RE's.  The camera seemed to be better positioned than the others, the weaponry more diverse, the enemies more interesting, and the challenge to be just right.  Capcom took a huge gamble with this port and ultimately lost, but to get one of the finest PS1 games on the N64 was a special treat in itself, and I think NP should have considered it to be somewhere on their list.

Onto Part 2!