Now you maybe on to something here. It would be a much younger Ganondorf (duh) but right now, he's sorta stuck in the middle. Like, yeah, he's a pretty bad guy, but he's not completely evil yet. Remember a male Gerudo is only born every century. He's journey through out the desert for power is not so much about him (yet) as it is for his people, to make sure that his tribe/people live on and are recognize by western civilization (i.e. Hyrule). Through out his journey (much like other Zelda titles) this young Ganondorf does not only scour the desert, but other lands, going through dungeons and temples to find clues to this "unknown" power. And through out the entire game you make important decisions, slowly the man transforming the man into the villain that we all know and despise today.

This is but a quickly thought up concept though, I'm sure the rest of the holes and details would be filled out later.