Well, I've seen several theories that the Trident is actually "possessed" or "harboring" Ganon's soul, or that the Trident is some sort of manifestation of Ganon.
This would explain why whoever holds the Trident becomes the "King of Darkness", the same title used of Ganon.

Up until a few weeks ago, I thought it was all pointless speculation, but this, plus the possibility of Ganondorf escaping the Seal by means of a soul-split makes me think it's possible.
Somehow via soul-split, Ganondorf escaped the seal, and the "Ganon" spirit in him was harbored in the Trident. Thus, when the Ganondorf from FSA takes the Trident, he becomes Ganon.

Either way, do to the inequality of Ganon deaths to Ganon appearances, I'd say FSA Ganondorf is a reincarnation...especially when you consider that he's not present or mentioned in MC or FS, suggesting that he was not known [which he would be if he was a Ganon from any other the games]

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Voted as Best Zelda Theorist in the Summer '08 Awards. Thank you to all who voted, and to all who inspired me along the way!