Why not have a game where you play as Link, Ganondorf, and Zelda.
The story could be that the reincarnations of Link, Ganondorf, and Zelda, who have no memory of the past and they all live in the same village, become best friends when they are very young. One day they are playing a game when they come along the entrance to the Sacred Realm. Once they enter, the triforce symbol on there hands appears and starts to glows. Then each triforce part emerges from there hands returning the triforce to it's original state. After that, the gods appears and sent all three kids to different parts of the world, at least one of them ends up and somewhere other then Hyrule.
So then you get to decide who you want to be first Link, Ganondorf or Zelda. Each of them goes through 3-4 unique dungeons, gaining a unique item in each one, on their quest to return to there village. Once you make it back to the sacred realm as one of the children, you take control of the next one, then finally take control of the third one. Once they all make it back to the Sacred Realm, at the same point in time through different entrances, you get to choose which character you use for the rest of the game, and that character touches the triforce first. Once your character reachs the triforce, it again breaks into three pieces.
You then at that moment get to fight one of the two remaining children, the one you don't fight becomes the final boss. Once you defeat the child you choose, you get there triforce and items. Finally, you go through 4-5 more dungeons before finally battling the final boss.
Once you beat the game, you have to choice of going back and making different choices for a different ending. The last 4-5 dungeons you go through will be the same no matter who you choose, but you will have to get through them completly different ways depending on what items you have.
That's all I can think of, it may not be much, but if you added the right elements I think it could make an amazing game.