I don't know if a whole game starring him as the main character could work...but maybe a part of the game where the player has to play as him might. Like perhaps there is a moment in the game where you learn about his past and you play as him when the game is going through his memories. The same sort of thing could happen with Zelda, like perhaps she has to escape the castle or something. This could add quite a bit of character development.
Wreak havoc as Ganondorf, bring chaos and dismay upon the peoples of Hyrule, and obtain the Triforce whereupon you transform into Ganon and have a duel with a some kind of enemy (lol Link) before winning and ruling the world.