Except instead of good and evil uniting for a greater force, I liked the idea that this game is set in the future and the characters just grew up together this time.
We've had Zelda grow up on a Pirate ship not knowing who she was, why not have Link and Ganondorf, Zelda too even, just as childhood friends, who one day have these elements of the triforce glowing on their hands and set off on an adventure.
In a different series, this could be where you decide who you play as, but I can't see Nintendo doing that.
Maybe they find out the past and Ganondorf turns against them, or maybe they're such good friends he breaks with tradition.