The Legend of Zelda: The Wind Waker is the ill-fated Zelda game that was released early in Gamecube's lifespan. It wasn't finished, but instead rushed out for reasons that few will ever understand.
The main flaw that many people think of is the sailing. It is incredibly boring, unless you have one of those box-in-screen thingies [1]. Though there are ways later in the game to speed it up, you might as well get used to sailing.
Of course, what really makes everyone hate it is that it was a cartoony graphical retool of an industry magnum opus (Ocarina of Time) ported onto what was unanimously agreed upon as Nintendo's weakest console in their history at a time where the company was suffering from major scrutiny for being seen as kiddy.
May have caused Cloud's 2003 poll victory due to pic factor. And is contentious to the point of inspiring revisionism.