Although I kinda doubt that Ganondorf will actually be in SS, I do have an idea or a hope that he will appear in the game. I believe that if he does appear in the game, that his role won't be that of a villian, but yet of a young Gerudo child/teenager who is being groomed to become the future ruler of the Gerudo theives. I think that he and Link may cross paths a few times in the game, maybe even with Ganondorf helping him out a few times (yes, I know crazy, but hey I think that during this time, he isn't the power-hungry demon that we all know him as). Also maybe along the line, we'll actually get to see what caused Ganondorf to become such an evil guy. I believe that there's got to be something more than just him being jealous of Hyrule's lush lands that triggered him to begin hungering for the Triforce. Maybe something really bad happens to him during the course of the game or maybe after researching ways of trying to get Gerudo Valley to prosper or during the course of his training to become ruler, he discovers the Triforce's existance and then begins to develop a lust for it? I don't know, but I believe that we'll find out if he does appear in the game.
Anyway, yeah, that's what I think his role will be in SS.