Well, I've been skimming over the actual reasons for the backlash since it includes spoilers, but generally the complaint I've heard most was that it's essentially a giant Ocarina of Time Fanservice with too little exploration. Another site said that it probably had the best storyline of any Zelda game, but the storytelling was horrible.

(I'm not going to touch any of that until I finish the game, though.)

And the Wind Waker backlash was primarily because of the graphics. Once people got passed (or wrote the game off for) the way it looked, Wind Waker was generally well-liked. Largely because it has the best climax of any game in the series.