I think it's an incredibly invalid argument that Ganon's in too many games. He's only been a final boss in seven games (counting only one Oracle game) out of fifteen so far - that's not even half! Besides that, he's the main villain of the series. We're not getting rid of him that easily. The games that don't involve Ganon in the story are generally considered side-stories. There are two exceptions (The Minish Cap and Spirit Tracks), but that's okay since TMC is giving background to a different game's backstory, and ST is developing its own side of the timeline, with its own different Hyrule and villains. I would think that some Zelda fans would be very happy about that.
Considering Zelda Wii, however, I don't entirely expect Ganondorf to reappear. It depends on whether or not it's a direct sequel to Twilight Princess. If it is a direct sequel, there's a low chance of him appearing. Even if it's not, I doubt it will be GanonDORF. Nintendo has been pretty consistent with his human form dying once in each timeline, so if Zelda Wii is a distant sequel to Twilight Princess, then chances are that Ganon will be there. Getting rid of him would make little to no sense. I imagine they'll do something to explain how beast Ganon appears in later games.
It may be, however, that Zelda Wii goes somewhere in the timeline that we're not anticipating. In that case, Ganon may or may not be in the game. I think it still stands that Ganondorf will only appear in human form if it's before Twilight Princess (or maybe if he's shown in a flashback).