I'll mainly address my thoughts on the question of whether or not Ganondorf is an overused antagonist. I'd have to say no to that. I think Ganondorf still has a lot to offer as the Zelda series' main villain. Doing away with him obviously isn't a smart move by any means, but that doesn't mean he should be used on a whim of Nintendo without making his appearance actually worthwhile. I think the way Nintendo portrayed Ganondorf in Twilight Princess was great. However, as Axle and others have previously said, he was just thrown in at the last minute or something, when he really wasn't needed to make the game good. Zant's character was a little quirky at the end, but overall he was a pretty badass villain and fit the story very well. Ganondorf could have been a really good antagonist for TP as well, if the story was built around him as the main villain.
Let's face it, we're going to see good ol' Ganny again sooner or later, which I think is good, but whether or not he will be used well is questionable. And as others have said already, Ganondorf will most likely not be in Skyward Sword, seeing as it takes place much before his time. We may see a referance or foreshadowing of Ganondorf (which I think would actually be pretty cool if done right), but we can safely say he won't be our main bad guy.