Well, like a few other users said, it's been a 100+ years since OoT and I'm betting that when Ganondorf returned, he could've changed quite a few things.. Tell me why it shouldn't be different?
Anyway, I've just started playing TWW again a little while ago and remembered again why it's such a cool game. Though I've always been slightly miffed at the lack of dungeons (there are what? 5 or something?) and at how easy everything is... And then there's the boring Triforce of Courage-hunting... But oh, well. Guess you can't have everything. Let's hope Twilight Princess will fix all that.