Well, I don't expect him in the game but this idea that Skyward Sword reveals the origins of the master sword throws a massive kink in timeline theories everywhere. According to the A Link to the Past manual storyline, "Suspecting that Ganon's power was based on the Triforce's magic, the people of Hyrule forged a sword resistant to magic which could repulse even powers granted by the Triforce. This mighty weapon became known as the blade of evil's bane, or the Master Sword." This leads me more and more to think that there is no universal timeline. Rather, I think that there are several. For example, OoT, WW, and the DS titles all fit in one continuous story. In this light, I don't think that we can expect Ganondorf. We've already heard about the origin of the master sword. If this is about that, it's probably a completely different story. Perhaps it's specifically pre-OoT, but I don't think that's definitive.