I believe that Agahnim and Ganon were the same person. Remember, Ganon wished on the Triforce to let him rule both worlds. When Agahnim disposed of the King of Hyrule and the Seven Maidens, he technically was the ruler of Hyrule, even though he never got to destroy it. I take it that Ganon managed to incarnate himself in Hyrule thanks to the Triforce.

For me, I pronounce Agahnim A (as in apple)-guh-nim (as in them). When I say his name quickly, it sort of sounds like A Ganon, as in an incarnation of Ganon.

Finally, though alter-ego has two meanings, Ganon's spirit rising from Agahnim's corpse seems to be saying that the use of alter-ego in the matter was that of being the same person.

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