To put it simply, no. Ganondorf is fine and dandy, but he's been used far too much to fit SS's theme of innovation and freshness. Also, I still don't forgive him for what he pulled in TP. Just kidding, but still.
If this is to predate OoT and give us the origins of the Master Sword, then there is next to no chance of Ganondorf being in SS. He originated in OoT most likely, and if this is to explain the Master Sword's origins then he absolutely cannot be a part of the game.
And for those of you who say that the Master Sword is only useful against Ganon/dorf and that it wouldn't make any sense for there to be a villain, remember that the Master Sword contains the power to repel evil, not the power to repel Ganon. It's just that whenever you think of the Master Sword in use, you think of Link's many struggles with Ganon.