We could definitely see Ganon again by my timeline:
CT: OoT--MM--TP--FS/FSA--ALttP/LA--LoZ/AoL--OoX
So we know what happens in the games that Ganon/dorf is in. Those that he is not have their reasons, like in MM how it wouldn't even make sense to have Ganondorf in Termina and FS we know Ganondorf is around since it prequels FSA but he just didn't do anything big in FS. The gaps are the places in question and there are two big gaps that I think most people have no clue what Ganondorf was doing at the time or, for lack of a better word, how he came to be what he was in the game after the gap.
Personally I think there could be a killer game to take place between FSA and ALttP here, possibly leading into the Seal War. There's a huge plot hole in my timeline that has Ganon (pig) being sealed in the Four Sword then later in the Seal War Ganondorf (man) breaking into the SR and getting the power of the Triforce. I think a game here could answer some questions and include Ganon/dorf as well, though it would probably not end like most Zelda games. The ending I think would be best if it showed Ganondorf successfully gaining access to the SR but then showing it seal up.
Ganon could also be involved in a game that would take place between ALttP and LoZ. Another mystery is how Ganon was able to come back in LoZ when he was killed the very same way in ALttP, however for some reason in LoZ he stayed dead. Conclusively, it only makes sense to assume that his defeat both times had the same results, though he somehow returned in LoZ and I would like to know how. Again, this could be a neat twist to an ending for a Zelda game rather than having the traditional "beat Ganon and save Zelda" scenario.
As for SS, this discussion isn't specifically about that game but because I don't believe there have been more than one Ganon/dorf throughout the series, I doubt he will show up. I believe OoT to be the first instance that Ganon/dorf does anything in his history.