Overall, I'd have to say Twilight Princess is the better game. Now which is a better Zelda game...? That's a different argument.
The reason I say TP is because I feel that TP tried to appeal not only to us Zelda fans, but bring in outsiders to the series as well. A game that succeeds in appealing to a more broad audience would be the overall better game. I noticed a while back that a good amount of recent Zelda joiners would say "Twilight Princess was my first Zelda game and I loved it!" Wind Waker was a fantastic game, but its cartoony atmosphere, cel-shaded graphics, and endless sailing are things that appeals more to us Zelda gamers than others. Twilight Princess on the other hand was easier, allowing non Zelda players to adjust to the concept of puzzle solving, it was empty yet vast, giving gamers a grasp of the beautiful environment but not overwhelming them with too many secrets, and it had a rather dark and deep storyline with impressive character development, which is what the audience wants now adays. TP was also more "real" in that it didn't do as much things and just throw magic as its excuse. The game actually leans away from magic and goes heavily toward technology. Us Zelda fans are used to magic being the excuse for everything, but other gamers shake their heads at it. Most magic that was in TP had rules making it more appealing to the average person.
We still had the classic trio acting like themselves, but their personalities were changed to be more appealing. Link was a bit more "perfect" to appease the fan girls but he still had some growing to do as with most Links, he's just a kid. Zelda had more authority about her, changing her from a princess to a queen, yet she still held that compassionate atmosphere her reputation has gained her throughout the series. Ganondorf is still a conquering genius, but for once he's not focused on the Triforce. He has the power he wants, he only needs to make sure he can keep it. There are plenty more examples, but I'd be here all day.
Twilight Princess did all this while still maintaining a Zelda feel by throwing all sorts of hints to Ocarina of Time (considered by many to be the ultimate Zelda game) with its visuals, puzzles and music.
Wind Waker is a fantastically rupee game, but it overall doesn't seem that appealing unless you're a Zelda gamer. Twilight Princess on the other hand succeeded in appealing to both Zelda fans and general gamers.
