Wind Waker was perhaps the worst Legend of Zelda game I have ever had the displeasure of playing. To simplify the matter, let us look at the major drawback of each game:

Twilight Princess: wolf form
It was pretty bad when you were forced to play as the world for extended periods of time throughout the first half of the game ((SPOILER)Lanyruu Province anyone?), but afterwards it wasn't that bad.

Wind Waker: sailing
Worst game mechanic ever. Seriously, even once warping became available, it was the most painful manner of getting around the world ever. The tedium just about ruined an otherwise good game for me.

If Twilight Princess was up against Ocarina of Time, competition might be a little closer (although not in TP's favor).