As I said earlier, and if you played/know the quotes from FSA, it is a different Ganondorf, but still the same Ganon(read: evil spirit).
It makes perfect sense if we consider Zelda saying that Ganon is an ancient demon reborn, and if we place FSA after TP, makes sense because we all saw Ganondorf dying at the end(or at least what appeared as a death)
It makes perfect sense if we consider Zelda saying that Ganon is an ancient demon reborn, and if we place FSA after TP, makes sense because we all saw Ganondorf dying at the end(or at least what appeared as a death)