Coming from a interview with IGN.

“From early on we were thinking that this was going to be the earliest story in the Zelda series, and it didn’t really make sense for us to have Ganon appear in this game. Obviously he makes his first appearance later and that would kind of confuse things, and so in terms of determining, ‘well then what are we going to do with who the antagonist in this game is,’ the answer that we came up with is this kind of strange character, Ghirahim, somebody who you can’t really tell is a man or a woman.

 

“So he’s sort of this character throughout the game that you’re fighting against who plays the antagonist role but his ultimate goal is trying to revive a greater more evil being than himself. So, you know, that’s perhaps something that might later have connections to Ganon and things like that, but from early on in this game, we knew that that wasn’t going to be the focus with this story.”