Quote Originally Posted by Kawaii Ryűkishi
You could try to reconcile the discrepancies with split timelines or whatever, but that's a level of convolution clearly not intended by the developers.
Quote Originally Posted by http://www.zeldalegends.net/index.php?p=233&style=tww
Q: Where does The Wind Waker fit into the overall Zelda series timeline?
Aonuma: You can think of this game as taking place over a hundred years after Ocarina of Time. You can tell this from the opening story, and there are references to things from Ocarina located throughout the game as well.
Miyamoto: Well, wait, which point does the hundred years start from?
Aonuma: From the end.
Miyamoto: No, I mean, as a child or as a...
Aonuma: Oh, right, let me elaborate on that. Ocarina of Time basically has two endings of sorts; one has Link as a child and the other has him as an adult. This game, The Wind Waker, takes place a hundred years* after the adult Link defeats Ganon at the end of Ocarina.
Miyamoto: This is pretty confusing for us, too. (laughs) So be careful.