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Welcome to Overrated Vs. Underappreciated.  In this special Zelda edition, I'll talk about what I think the most overrated Zelda game is, as well as the most underappreciated.

OVERRATED - Legend of Zelda: Wind Waker (GC)
Nintendo's first GC Zelda was a shock to many people.  It abandoned the realistic look of Ocarina of Time and Majora's Mask in favor of a more cartoon-esque style, and many "hardcore" fans decried the change and painted the game as a kiddish coated waste of a Zelda title.  Once Wind Waker was released, though, many of those said haters changed their tune, raising this Zelda well above most others in the franchise, coughing up Game of the Year awards to the now "awesome!" game.  In fact, the glory Wind Waker has obtained has swelled to the point that it laid claim to Nintendo Power's 4th greatest Nintendo game of all time.
Before I begin my argument, I would like to state that Wind Waker is NOT a bad game.  It looks really good (I never thought the look was not Zelda...it reminded me of what Link to the Past might have looked like in 3D), has some great music, features some of the best battle controls in the whole series, and has some clever boss encounters.  All and all, Wind Waker still stands head and shoulders above many other games.
But, Wind Waker is saddled with several glaring issues that plunge the enjoyment factor into one of the game's many whirlpools.  No matter how much fun Link is to control, you'll spend half the game stuck in a boat.  And that boat is the main factor in the game's downfall.  Sailing is a novel idea, and for a time, it proves to be droll entertainment.  However, the vast oceans that spread apart the game's towns, dungeons and other key locales begin to grow weary the more you sail on them, and after a while I began to read books instead of controlling Link's direction.  It takes too long to get anywhere.  Even the game's warp function is too crippled to be of much use.  And once you get to the part in the game where you need to sail around looking for Triforce shards, the sailing's dullness evolves into annoyance.  Both a game design flaw and a way to cheaply add length to the game, the "Tingle Triforce Shard Parade" (as I refer to it many times on the site), will have you spending hours pinpointing various spots in the ocean, circling around the exact point you need to scoop up the chest, warp back to Tingle Island (or, if you're unfortunate, sail back over there), fork out Rupees to have him translate the map you found, and then again sailing out and try to find the shards lost in the vast sea.  And some of these charts are not stuck in the bottom of the depths, but are reachable only through certain sidequests.  And you need to keep gathering Rupees to let Tingle keep deciphering these important parchments. As a piece of gaming design, it sucks.  Badly.
Between the immense amount of sailing, though, there are the enjoyable parts where you control Link wandering about the game's islands, beating enemies, solving puzzles, chatting to islanders and such.  Most of these moments are great, and even tops Twilight Princess in terms of its battle engine.  Link isn't quite as versatile in TP as he is in WW (the lack of a secondary weapon button is one reason, and the reaction time between switching the various tools in Link's arsenal taking longer in TP is another), and battling Moblins and other baddies is a lot of fun.  And the dungeons are also fairly good...except for the two where you're stuck with AI controlled Sages-To-Be in the hopes of getting them safely to the end of the dungeon.  The Wind Waker is used to control them, and the tune you're required to play before you can move them on your own is a bit long.  Along with that, they don't control all that well, so it just doesn't add up to joy...especially compared to the game's earlier, better dungeons.
Wind Waker is a good game that has problems.  No game is perfect, after all.  But in all honesty, to give Wind Waker Game of the Year awards or high marks on your Top Lists of All Time is a little silly to me.  The game's tedious sailing, unnecessary length and poor implementation of dungeon allies easily dethrones it...especially in Nintendo Power's case, which pretty much stunned me.

UNDERAPPRECIATED - Legend of Zelda: Four Swords Adventures (GC)
The second Zelda GC game is the one most people forget about.  Crippled from mainstream access due to the required GBA links to add in more players, Four Swords Adventures nevertheless is a great piece of gameplay goodness and, alas, a tragically mistimed execution by Nintendo.  If only they held back on this game until the DS arrived, then maybe the game would have done better commercially.
At any rate, the game uses the Four Sword in a great manner, offering up a bunch of neat puzzles that require teamwork to topple.  Even playing the game alone proves to be rewarding, thanks to the 4 battle formations you can pick.  The change from a traditional Zelda adventure to a more competitive quest to gather Force Gems is a lot of fun, and my wife and I have enjoyed our time playing the game quite a bit.  The visuals, despite mostly being plucked from Link to the Past, are well suited for the game, and there's some nice quality animations, too.  You can't keep items and heart containers, which may have bothered some, but for this game to work, it had to be done.  If one player was able to keep all of their Heart Containers, the game would become a contest to get them, and that wouldn't be much fun.  The game also does use its GBA requirement well, since you can enter houses and caves at your own discretion, letting your friends search up above on the main playfield as you look for Force Gems underground or indoors.  
All and all, despite shedding some of the usual Zelda rules, FSA remains a well designed title that's pleasurable to play.  It is one of the GC's better multiplayer games, and stands up well enough on its own merits as a solo affair.  You can probably find it pretty cheaply nowadays.  The GBA requirement makes the game a bit difficult and costly to fully enjoy its potential, but I still recommend giving it a go if you can.