Wind Waker has its qualities. Graphically one of the best looking GC games. Mini-games and things to do apart from the main quest was plentiful, lots of games in Windfall and around the Ocean. Downside was the Triforce quest, Sailing and the lack of inhabited Islands and the length of main story.
Twilight Princess had a great story, bit let down in places. As for things to do apart from the main quest, less than Wind Waker. This didn't even have a shooting gallery (
OOT,
MM and WW had one). The Fishing area is much improved. The areas around the main story inc side quests and mini-games let this down a bit, even though there were quite a lot of things to do apart from the main story.
Out of both titles, i can't pick one as the better as both had faults to them. I liked them both the same.