Skyward Sword was said to take place a few years before OOT where we first saw Ganon. In OOT Ganon had already gained some power and the Triforce was already in place. Some Zelda fans have started to expect we would be seeing Ganon in some capacity, maybe as a member of Link’s home village or something.

Skyward Sword producer, Aonuma, had this to say..

“Yes, that’s right. Ganon typically appears in a Zelda game when the story is centered around the Triforce. This time around, the Triforce sort of takes on a different meaning and plays a different role in the story. So because of that, Ganon will not appear.”