It's a tough choice, because I love both. I love the overall "feel" of TWW, the music, the graphics... But I love those things in TP, too. I think the dealbreaker for me is how tedious so many aspects of TWW ended up being. Then again, TP has its tedious parts, too, but they're mostly skippable. I just like to go for 100% with that game more than I do with TWW.
Wind Waker may have had the better exploration and music but Twilight Princess I thought was better in just about every other area. Better dungeons, better graphics, better companion, better story, even better challenge. Both games are fairly easy as far as the combat goes but Wind Waker is ridicuously easy at times.
Wind Waker. Probably my favorite game ever. Twilight was cool but is my least favorite 3D Zelda, while I find Wind Waker to have a gorgeous, radiant soul and to be darn near flawless. I never don't have a good time playing it.
The Wind Waker is one of my favorite Zelda games ever made with more involved characters, a beautiful art style, and a stunning climax...
But I prefer Twilight Princess. Ever since the release of Ocarina of Time, I've yearned for a successor and Twilight Princess successfully delivered. Midna is the greatest series companion, while Wolf Link portions are limited, the change in pace is welcome, and the return of franchise locales never gets old. The game has its flaws such as the not very useful hidden skills sans the Cave of Ordeals and Zant's weak end but these are so negligible as to not detract from the experience.
Neither of these will ever be my favorite Zelda game, but I had to give Twilight Princess, because I had to work so hard for that awesome ending. My save file got deleted somehow whenever I had made it to the Zant fight.
Twilight Princess is my favourite Zelda game. Wind Waker is my least favourite (of the 3D titles). I do still love WW to bits, but when comparing them together, I find that TP has less flaws and is the more enjoyable experience.
I didn't expect WW to win. But I also didn't expect it to get beat as badly as its getting beat either. 21 to 31? I'm stunned. Both these games have flaws. Both these games I've played and beat. Both these games I've developed emotional connections too. One of these games I love. Wind Waker for me was, basically my first Zelda, (if you want to get technical I did play a little OoT before but didn't remember it at the time I got WW. It was the first one I beat. Its what got me into Zelda, and I loved every minute of my first playthrough... well maybe not some of the puzzles but... Anyway TP on the other hand was a game that I got much deeper into my Zelda career, which isn't saying a lot since I've only been a Zelda fan for meh... 3 1/2 years, but anyway, I started playing TP and was just depressed by the colors and everything and it had such a SLOOOOOOOOW start. (Although you could say WW had a slow start as well, it didn't have quite such a slow start that I wanted to throw the screen through the TV before I got my green tunic and could actually enjoy the game.) We got Wolf Link, who in my opinion sucks. I hated Wolf Link, probably for what he's involved in, the spirit tears or whatever they're called, I hated those parts. Also the game was FAR too easy, granted in my last two playthroughs of WW I didn't die once but that's because I went out of my way too be careful both playthroughs just so I could brag to friends about not dying in a Zelda game. TP on the other hand I just don't take care of myself because I'm going to kill whatever it is anyway I shouldn't have that mindset. And THE BOSSES WERE EASIER THAN THE REGULAR BAD GUYS!!!!!! That is just wrong. Anyway I think I've probably ranted enough. In case you were wondering I voted for WW.
Twilight Princess. It took a bit for me to warm up to it, but I came to love it and I have fun with some of its dungeons, its boss fights, its locations. Its a beautiful game. Midna is a good and helpful companion on par with, and even surpassing Ezlo.
I think Windwaker is so damn boring. Its dungeons are boring, its islands are boring. Its boss fights are boring. The music is good and the art style is cute, but that's not enough to save it. I wanted to like it too.
I have a very strange answer... I'd rather play Twilight Princess... but I'd rather replay Wind Waker.
Twilight Princess feels more fun to control, has more active combat since you control the various special moves, has more item and combat options and applications. But it's also dark and muddy, and contains two of my most hated dungeons in the series for their sheer boredom. But Wind Waker, though simpler, with piss-easy combat and not much in the way of martial challenge is still more fun to exist in. The bright color and bounding music of the Great Sea just feel good.
Taking them on how I felt when I first played each one, I think I enjoyed Twilight Princess more. Wind Waker's dungeons were utterly brainless, while Twilight Princess' required at least some thought. But I've played through Wind Waker thrice as many times, simply because it was just more enjoyable for me to do so.