Hmm...how about this.
Zelda and Link are childhood friends from a random village, Link is kidnapped by a time traveler to get rid of a "hero clad in green", and she trains with the village ninja master to go on a quest to find him. A quest ensues, filled with the normal Zelda schtick modified for a ninja. As her quest goes along, she learns about what SHOULD have happened over the last few years. How SHE should have been the kidnapped one, how HE was supposed to be the hero, and right before the final castle, Ganon conquers all of Hyrule and essentially wins. Zelda finds out, however, that Link never aged due to effects of Ganon's time travel. She rescues him, steals Ganon's time travel thing (she is a ninja), gets Link back to the right time period, and battles Ganon in the past wearing green. Ganon dies, Sheik is mortally wounded, and ends up giving Link the sword he'll need for his future and dies.
Hey, why not? I'd play that.