Kairon, I'll never get to work on Zelda so what is the point of keeping secret what I wish to see experimented in future Zeldas. Honestly I never would have thought transforming into a wolf needed to be a Zelda game, it could have really been something different, but they seem to have adopted this theme, for at least one game, and it seems to work.
Ian, Wind Waker did screw up a lot of small things (Zoras), but I think it showed Ganondorf is reborn; and eventually one will be reborn following the stories furthest in the future of the chronicles (which would be part 2 I guess?).
Still, there could be a story where the Ganon of WW is resurected when a future Link pulls the sword out.