A lot of people's criticism for Ganondorf is very misplaced. He's the main villain of the series, and the whole overarching story centers around him being the villain. It's easy to understand him being missing in some games, but to eject him from the entire series would just be ridiculous, unless they can formulate a logical story-based reason for it.
For Skyward Sword, however, I'm not going to say one way or the other that I would or wouldn't like Ganondorf to appear, because there's no reason to consider it a possibility that he will be in the game. They've basically confirmed that Skyward Sword is a prequel to the entire series, or at least the existing chunk of the series involving the Master Sword. Because Ocarina of Time is (almost undoubtedly) the first chronological appearance of Ganondorf and involves the Master Sword already in existence, Skyward Sword has almost no way of involving Ganondorf.
Notice that I said almost. I can still imagine a few ways that Ganondorf might be alluded to. Perhaps we'll see an ancestor of his, or maybe Twinrova will make an appearance at a younger age and allude to something related to the male Gerudo king born every 100 years. Maybe we'll even see the male Gerudo king living before Gandondorf. It's possible that this Gerudo king could even be the main villain. I do not, however, consider it at all possible for Ganondorf himself to be the main villain, or even an important one. He's not even going to have been born yet during the main story.