They won't include Ganon(dorf) for multiple reasons, among them the fact that people are a bit fed up with him. He's been in every single Zelda game with the exception of some of the handheld games and Majora's Mask. Sometimes, he's the main villain from the start, other times he's been the secret villain behind what appeared to be the main villain. It's been done so many times that "
Hijacked by Ganon" has become a phrase slowly invading pop culture.
But for the sake of this game, let's play this through. How could Ganondorf hijack yet another game?
Well, time travel
is one possibility. Using some mcguffin artifact, he could travel back in time to erase the first Link from history, in the hopes of preventing the cycle of rebirth amongst his descendants. He can't kill Link's parents, because he can't reach Skyloft and they're safe there, so he has to lure the first Link down to Hyrule somehow. Which he does by using the puppet villain of the week, presumably the Kefka-looking dude from the GDC trailer.
Another possibility is having a young Ganondorf that learns of the prophecy that he will eventually conquer all of Hyrule. He would be a young boy, kind of like an Anti-Link. At the end of the game, he's defeated and put into some kind of suspended animation.
Or the dark interlopers put a spell on him that prevents him from dying. Every couple of decades, he reappears, claims to be his own son and takes control of the Gerudo tribe. When he can't hide the fact that he doesn't age any longer, he leaves the Gerudo "to raise his son", only to repeat the charade again and again.
I guess the most likely scenario is a weird dream sequence, half prophecy, half
big lipped alligator moment, kinda like the Dark Links scene from Twilight Princess. At some point in the game, we'll see what the future holds, complete with flashes to Ocarina of Time. I suppose there is even a way to tie this into Ocarina of Time 3D somehow.
Of course, that wouldn't make him the main villain. For that, you need to cheat. Either by using time travel, extending Ganondorf's age to ludicrous lengths or by doing something like... That new character from the GDC trailer ends up morphing into the giant warpig form that we associate with Ganon. He gets sealed in the Triforce of Power somehow, and when Ganondorf touches it, they somehow merge, which would mean that it was this other guy all along that was the bad guy. And then a later retcon could flip this, establishing that when Ganondorf touches the Triforce and they merge, he lives through new guy's memories or something. It's magic, they'll find a way. If they want to.
There are tons of ways to shoehorn Ganondorf into the game. But I really don't think they should do it.