I'm actually quite shocked by how many people think Twilight Princess is better.
In my opinion, The Wind Waker was way, way, way better than Twilight Princess. Twilight Princess was too easy for me (although, admittedly, I WAS older when I played TP) and I really preferred the graphical style of WW. The Wind Waker feels like a much more emotional game, and while it might not be as realistic as TP, I think the characters were a lot deeper and more expressive. The plot, as well, was more creative and shocking. To some extent, I think that Twilight Princess was repetitive and the wolf thing, while incredibly awesome at first, became boring quickly. Midna really did make that game.
Plus, The Wind Waker had a lot more exploration. Occasionally, I'd find those caves in Twilight Princess to explore – you know, the ones that would give you a Heart Piece or Poe or something. You know what I called them? "Wind Waker caves." They reminded me more of the previous game that the actual one I was playing. Twilight Princess had a big world to explore as well, but it was all made pointless by the usually small rewards you received, the emptiness, and the warping. With WW, I actually felt compelled to sail across the whole world and complete my Sea Chart, just for fun – and I still don't think I've thoroughly explored every island. I think the only reason I actually wandered across the world of Twilight Princess was the fact that I wanted the heart pieces.
I feel like a lot of my arguments are kind of cliché against poor TP, but I really do feel that way about it. Of course, I love Twilight Princess; I've actually replayed it more than The Wind Waker, but that's mainly because I can actually handle its difficulty. XD And it's awesome, one of the best video games out there... but I just love Wind Waker so much more.