I'm a little turned off the art style of Skyward Sword. I'm a huge fan of the Twilight Princess/Ocarina of Time style. Other than that though, I think the game is shaping up to be amazing.
Ganondorf won't be in the game it was confirmed by Nintendo Power, which is fine by me because I'm actually sick of all these "reboots" despite them being awesome games.
In games like Twilight Princess I was fine with it. They did a good job of explaining just what happened to him at the end of OoT and how he was able to return. But I know what you mean. In some of the games it just seems like "Ho ho, Ganon is doing dastardly things. Stop him!"