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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 the list, either.  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 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 2 covers the Game Boy Advance through the Wii.  Part 1, which can be accessed here, covers the NES through the N64.

Game Boy Advance
A few eye-raisers that compelled me to begin this feature are buried in this list.

1. Metroid Zero Mission
I think the one bit that inspired all of this ire within me about this list is the comment that Metroid Zero Mission is the best Metroid title in its long existence.  Um....no.  It is a great game, don't get me wrong.  I count it highly among GBA games, and it was on my Favorite Games list when it was 30 games.  But better than Super Metroid?  No.  Super Metroid is the pinnacle of 2D gameplay in my eyes, as I mention on my Favorite Games article about it.  It is as close as the 2D world has gotten to creating an organic-feeling environment, one that really feels like it's alive.  It's quite impressive.  Zero Mission doesn't manage to emote the same feeling.  The Power Grip also adds in some frustrations; what if I didn't WANT to grip the side of a platform?  Too bad, because if you're near the edge, you're always going to grab it.  Part of the mythos has been retconned with Kraid's new large size in M:ZM.  Lastly, there's a bit too much focus on the speed booster to uncover hidden powerups.  I do believe that it's a fine addition to the series, but it is not the best Metroid title by any means.

2. Castlevania: Aria of Sorrow
I applaud NP for placing Aria at #2.  It certainly deserves such high recognition.

3. Mario & Luigi: Superstar Saga
I think I'm in the minority when I say that this game is a bit of a train wreck gameplay-wise.  I really dislike the way each Mario brother is forcibly assigned a button both in combat and in exploration.  It's incredibly easy to get them mixed up, and it becomes very frustrating, especially as the game gets near its conclusion.  It's a novel idea, no qualms about that, but it could be much better implemented.  I will not knock the humor though - that was top notch.  But humor does not a good game make.  It's a bit of a disappointment to the Mario name, in my opinion.

4. Astro Boy: Omega Factor
Another kudos to NP for including Astro Boy so high.  This is a triumph of action gameplay, packed with tons of secrets and some great challenge.

5. Legend of Zelda: The Minish Cap

6. Warioware Inc.: Mega Microgame$

7. Gunstar Super Heroes

8. Drill Dozer
Gamefreak did produce a very unique game here, and I'd agree that it is worthy of such a lofty placement on this list.

9. Metroid Fusion

10. Advance Wars
I can not get into Advance Wars.  I find its plot boring, its lack of character connection a problem, and thus, the gameplay has no motivation to me.  Fire Emblem in my opinion is infinitely better.

11. Pokemon Ruby/Sapphire

12. Castlevania: Harmony of Dissonance
Whoa whoa, back up.  Harmony is probably the most cumbersome Castlevania following the SotN formula.  It has a castle that is too huge, a magic system that is too trial-and-error, and the most basic gameplay engine of the handheld line of CV.  It shouldn't be on the list at all in my opinion.

13. Golden Sun
Golden Sun didn't do much for me, personally, but I can see why people like it.  The battle system wasn't engaging enough for me, and the puzzles got a little on the tedious side.  But it is a good game, I won't knock that.  Just not my favorite.  I'd have it a bit lower, myself.

14. Mega Man & Bass
A bit of an odd choice, considering they usually have avoided ports on this list.  That said, Rockman and Forte didn't come out for the SNES here, so I guess that's the reasoning behind it.  At any rate, the sacrifice made to the game's screen size makes MM&B more difficult than it ought to be.  The core gameplay was fine (and Bass was fun to play as), but I sold my copy, so I guess that shows how much I cared for it.

15. Fire Emblem
It's a shame Fire Emblem is so low here.  It deserves Top 10 placement.  It really does.  It's the finest strat-RPG I've played.

16. Mega Man Zero 2

17. Golden Sun: The Lost Age

18. Mario Golf: Advance Tour

19. Mario Vs. Donkey Kong
Another "huh?" choice.  When you play the GB Donkey Kong, you'll understand why.  This game's controls are too slippery for what the game's trying to have you do, and comparing this to the earlier DK will showcase how that is a bad thing.  DK had the controls down pat.  The mere fact that Mario feels like he's ice skating here is a problem.

20. Wario Land 4

Some Notable Omissions:
Fire Emblem: The Sacred Stones
While easier and not quite as well-produced as FE, Sacred Stones remains a fun game to play through.  In fact, some people may like it more because of its monster dungeons to help aid in leveling up your troops, and its map screen.  I vastly prefer the original, but I think the sequel deserves some merit over some of the other GBA choices on NP's list.

Gamecube
I think that this list is by far the worst selection of the bunch.  Why did they skip some of the best games I've ever played for some of the worst?!  I can't begin to wrap my head around it...well, a brief aside to my thoughts.  I consider the Gamecube as Nintendo's oddest in terms of their treatment of their power franchises.  The first proper Zelda and Mario games did not wow me like I expected them to, and I found several third party games to be of much higher quality this gen.  But...I digress.  Onward!

1. Resident Evil 4
*clap clap* If any game for the Gamecube deserves to be #1, it's Resident Evil 4.  What a phenomenal game.

2. Legend of Zelda: Wind Waker
Whenever I see Wind Waker so high up on any Nintendo Power list, I really have to wonder (much like I did with Jet Force Gemini on Part 1) if they played a different game than me.  A "Director's Cut" that removed all of the obnoxious parts that broke the game off from the pedestal of Zelda excellence.  One where sailing was less important, or at least had more warp points to choose from.  One where the Tingle Triforce Shard Parade was noticeably absent from the game.  One where two of the dungeons freed you from having to control poorly done secondary characters who can barely defend themselves.  Hey...I think that game was called Twilight Princess!
For the record, I do like Wind Waker, despite the constant potshots I take at it.  I like the art style (it works, considering what a remake of the original or Link to the Past could look like), I like the music (it's excellent), I like the combat system (best in the series!), and I like the early dungeons a lot.  But the whole experience is mired by some very poor design choices, and that does not make this game worthy of being #2 on this list.

3. Super Smash Bros. Melee
Melee is a great game, no doubt.  But Brawl is better.  Much better.  So much better that it nearly negates Melee, much like how Melee did to the original.  I would myself put it lower on the list, if at all at this point.

4. Metroid Prime
The best game Nintendo put out on the Gamecube.  No griping here.

5. Soul Calibur II
I must be one of the only people who thinks that SC and SCIII are way, way better than SCII.  (I'm pretty sure I'm the only one I know that prefers SCIII over II, anyway).  The stage design is too cramped up compared to the other two, and I felt SCIII made more strides with its new characters and features than SCII did.  Sure, Link's here, whoop.  But I wouldn't have SCII on my list at all, personally.  I just felt unhappy overall with it.

6. Super Mario Sunshine
I was REALLY let down by Mario Sunshine.  Horribly, in fact.  I don't know if I've ever been so disappointed in a Nintendo game as I was with this one.  The hover pack, while novel, became too much of a focus point, and cleaning up tons of gunk got boring after a short while.  The enemy design was rather lackluster (and some were lazily cobbled together like a VERY early 3D game, for that matter).  I didn't connect to the world all that much.  The final fight with Bowser was dumb.  The camera was incredibly dense and poorly implemented.  And the secret stage setup was awful.  Stripping away the key gameplay mechanic of Sunshine is bad enough, but having to reclimb back to some of these torturous locations if you failed was purely idiotic designing.  In short, this is easily Mario's worst outing in my eyes, and is not anywhere near worthy of being on a Top Gamecube list.  There's too many other games put together far better than this disaster on the 'Cube to even consider it.  It had some good moments, but nowhere near enough to counteract its problems.

7. Pikmin
I like the sequel more, but I won't knock the original's placement here.  It's pretty fun stuff...I'd have it lower, myself, though.

8. Paper Mario: The Thousand Year Door

9. Resident Evil

10. Viewtiful Joe

11. Beyond Good & Evil
If this was up a few pegs, I'd be ecstatic.  I gush about BG&E's quality enough on this site, however, so I'll refrain this time. :p

12. Mario Kart: Double Dash!!
Oooooooooooo, how I hated Double Dash. XD  I still find Mario Kart 64 to be the best in the series, and this game's poor track design, forced "special" items and grating music pretty much confirm my mindset.  I still don't understand the hype of this game.  I didn't when EGM scored it so high, and I remain dumbfounded why NP even put it on their list.  At least it wasn't in the Top 10, I guess.

13. Billy Hatcher and the Giant Egg

14. Luigi's Mansion
A good game, yes, but not one of the best.  LM is a little too simple to be called that.

15. Metal Gear Solid: The Twin Snakes

16. Prince of Persia: The Sands of Time
Another fine game that should be higher up.

17. Skies of Arcadia Legends
Heh, my favorite game of all time!  You probably would predict that I'd be all "put this on top!" (and well, I guess you'd be right :p ), but I'm ultimately happy that it made the list at all.

18. Donkey Kong: Jungle Beat

19. Animal Crossing
Animal Crossing is quaint, but I don't consider it to be much of a game, really.  And man, can it become the absolute definition of "repetitive."  I wouldn't have it on my list, let's just put it that way.

20. Super Monkey Ball

Some Notable Exceptions:
Tales of Symphonia
Of all of these, this one startles me the most.  Considering that Tales graced the cover of NP, got a ton of coverage from NP, and got great scores from NP, to then suddenly omit the finest original RPG the 'Cube received from their own Top 20 list?  Gripping combat, likable characters and a heaping amount of questing add up to a fantastic RPG that should have been on this list without question.

Fire Emblem: Path of Radiance
I enjoy Path of Radiance (and one day I'll actually beat the silly thing) a lot, and it's a great strat-RPG with its own personality compared to the GBA titles.  It may not have been much of a looker, but I feel that the gameplay's strengths more than make up for that.

Legend of Zelda: Twilight Princess
Yes, I'm aware that NP plopped the Wii version of the game high on their Wii list, and that's fine and dandy.  But the Gamecube version, the original vision of the game before they reversed everything around, is the finest Zelda the 'Cube has overall, and should have placed on this list too.  I'm sure the Wii version disqualified it, though, so I won't moan too much.

Incredible Hulk: Ultimate Destruction
Why the best licensed super hero game I've ever had the pleasure of playing is not highly featured on this list is another conundrum.  The amount of pure joy that pours out from this title is immense, the gameplay is well balanced and fairly tight, and even after beating it it's fun to just run around and destroy things.  Should have been on the list!

Legend of Zelda: Four Swords Adventures
I'm a champion for this oft-overlooked Zelda.  I think that Nintendo should give the concept a second try on the DS or Wii, because I can see how much fun people would have with it based on my time with the GC attempt.  The GBA's make it more of a chore than it ought to be, but the overall level design was well thought out, and the gameplay is a lot of fun by yourself or with friends.  Bring it back, Nintendo!

DS
The DS list manages to be more solid than most of the others, but there's still a few games NP picked that don't quite settle right with me.

1. Elite Beat Agents
An excellent use of the DS hardware, EBA is a very challenging game that I can not play all that well. XD  But it's a lot of fun regardless.  A fine choice for #1, although I have other games that I find to be better above it on my own.

2. New Super Mario Bros.
A fine return to Mario's 2D roots, I'd have NSMB in the Top 10 myself.  Not #2, but definitely Top 10.

3. Mario Kart DS
After the Double Dash debacle, Mario Kart DS was a nice return to form in my view, with engaging new tracks, better music and a nice mix of retro tracks (that I would have picked differently, but that's just me).  The gameplay feels tighter, too, which is a plus.  I do wish the Blue Shell would have reverted to its MK64 version over the "big boom" MK:DD variant, but I have no other gripes.  I wouldn't have it this high, but it'd be on my list.

4. The World Ends With You

5. Tetris DS

6. Castlevania: Dawn of Sorrow
Ah, Dawn of Sorrow.  I really, REALLY wish that Konami did not force the Magic Seal system into the game, because it would have been stellar without it.  But, alas, it is there, making boss fights that are otherwise fun turn suddenly awkward as you grope for the stylus or quickly slide your finger across the bottom screen when you are prompted (and then trying to remember the silly Seal that you're supposed to use), making the otherwise great experience become jilted and aggravating.  Portrait of Ruin removed this shackle (and had a good gameplay engine with the two character angle), and Order of Ecclesia (which didn't come out until after this article was written) took Soma's Soul concept, tweaked it a bit, and built a great game around it, so both of those end up being better overall CV titles than Dawn is.  That's my two cents.

7. Contra 4
Nice to see Wayforward's remarkable revival up so high.  It deserves it.

8. Legend of Zelda: Phantom Hourglass

9. Phoenix Wright: Justice for All
NP has some sort of strange infatuation with Justice for All.  When the NP awards happened that year, NP ignored the superior Trials and Tribulations, resorting to JFA instead for some unbeknownst reason.  The issue I have with JFA is that it's, in my opinion, the weakest of the three Phoenix Wright games.  The script was embarrassingly rife with typos, the Psyche Lock system was at its worst (I highly prefer Apollo Justice's court punishment system, or the original PW's, for that matter), Moe the Clown made his Interrogation a nightmare, and I felt that the characterization was down a peg for the main cast (Franziska von Karma seemed to get the four star treatment in this game, though, easily providing the game's best moments).  Trials & Tribulations improved the Psyche Lock system, got the script back under control, returned Phoenix, Edgeworth and Maya's charms, and was far more engaging than JFA was. And then Apollo Justice came along and topped the whole PW saga the year this article came out!  So their choice of JFA as the finest Ace Attorney title makes no bloody sense to me.

10. Sonic Rush Adventure

11. Trauma Center: Under the Knife

12. Prof. Layton and the Curious Village
This delightful story-driven puzzler ought to be higher!

13. Castlevania: Portrait of Ruin
As should this improved CV title minus the stylus gimmicks!

14. Advance Wars: Dual Strike
I found this to be the best Advance Wars I've played, but the series still doesn't click with me. *shrugs*

15. Pokemon Diamond/Pearl

16. Ninja Gaiden Dragon Sword

17. Warioware: Touched!

18. Mario & Luigi: Partners in Time

19. Animal Crossing: Wild World

20. Cooking Mama

Some Notable Exceptions:
Hotel Dusk: Room 215
Oh, my sweet Hotel Dusk, why has NP ignored your noble heart?  A good question indeed.  This primo adventure game ought to have made it onto the list handily, what with its superb art direction, engaging plot and remarkable translation.  The game's clever uses of the DS's various features was also an achievement.  A tragedy that such a beautifully realized revitalization of the adventure genre was shafted by NP here.

Apollo Justice: Ace Attorney
Apollo Justice is the finest entry into the Ace Attorney series.  I loved the experience immensely.  But, as I said above, NP has some sort of freaky crush on Justice For All, so they passed over this vastly improved sequel for the weakest Ace Attorney of the bunch.  *sigh*

Dragon Quest Monsters: Rocket Slime
I really got a kick out of this game.  Taking a basic Zelda-esque gameplay concept, expanding upon it with a cool tank battling boss feature, and adding in a slick script with plenty of humor made this a keeper in my view.

Meteos
I'm not a big puzzle game nut, but Meteos switches the right parts of my brain to make it a joyous experience.  Perhaps it's the grooving music that accompanies each stage, or the great use of the stylus to slide your blocks around with.  I think it's a glorious combination of these elements, packed in with a wide abundance of unlockables and gameplay modes that seals the deal.  I like it a lot more than Tetris, at any rate.

Wii
I won't have all that much to say here, since I only own a handful of Wii games.  But I'll comment where I can.

1. Super Mario Galaxy
Galaxy is a revival of Mario's last good 3D outing (Mario 64) pushed to the stratosphere.  The game is easily the best overall title on the Wii (yes, I know, I have Brawl higher on my list, but I haven't beat Mario Galaxy proper yet), and deserves this spot.

2. Legend of Zelda: Twilight Princess

3. Super Smash Bros. Brawl
I loves Brawl.  I need to play it again. XD  But anyway, I think Sakurai has topped his two earlier efforts with Brawl, with its wide array of fun characters, clever stages and tons of unlockables.  There's some things wrong with it, but the overall package is solid.

4. Metroid Prime 3: Corruption
I'm having a hard time gelling with Samus here.  I think I prefer the Gamecube pad over the Wiimote to be honest, but I'll be giving this another chance soon.

5. Mario Kart Wii

6. NiGHTS: Journey of Dreams
My brief playtime with NiGHTS left me unimpressed...but I haven't gotten very deep into it...so maybe I just need to give it another shot.

7. Zack & Wiki: Quest for Barbaros' Treasure
Zack & Wiki is how one should do an adventure game on the Wii.  Ingenious level design, mostly responsive controls and a fun universe to roam around in, it's a real shame this bombed in retail.

8. Wii Sports
Eh.  That sums up my feelings as well as a paragraph would.  I like Wii Sports, but I have a REALLY hard time desiring to plop it on a list of the "best games Nintendo's ever had on its systems!"  If this was not a system-based list, it'd be nowhere on mine.  But the Wii has so little in terms of stellar gaming goodness on it (which is very tragic) that it's hard NOT to put Wii Sports, which was built and designed fairly well, onto it.  And there's the rub.  Eh.

9. No More Heroes

10. Super Paper Mario

11. Resident Evil: Umbrella Chronicles

12. Warioware: Smooth Moves

13. Fire Emblem: Radiant Dawn

14. Sonic and the Secret Rings

15. Boom Blox

16. Bully: Scholarship Edition

17. Okami
The PS2 version of Okami is majestic and awesome, and from what I've heard, most of that translated well to the Wii.  Another wise pickup, one way or another!

18. Wii Fit

19. Trauma Center: New Blood

20. Guitar Hero III

Some Notable Exceptions:
None in this case.  The Wii has only a limited number of solid titles, I own 8 games altogether, and only 2 (RE4: Wii Edition and We Love Golf!) aren't on this list.  I suppose I could make a mild argument for We Love Golf!, but the music and voice work is god-awful...and it's really just Mario Golf with a cast of generics and less interesting courses.  The core gameplay is a riot and well done, but I don't really think I could build a solid case for it with its faults.  It does provide a better golf game than Wii Sports, though...