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Unless his minions managed revive Ganon (Which is a huge possibility) there's no way that's the same Ganon. I'm 50-50 on the same-different theory. I think there's a huge possibility of him being different.

Ganon has been killed many times, just like there's many different Link's. in LoZ, Ganon is killed, because AoL, his minions are trying to revive him, if he didn't die, they wouldn't try to do that. Anyway, The Twilight Princess Ganon and the Wind Waker Ganon could be totally different people.