I have daydreamed about this myself, I will help if possible, I'm pretty ok at design. You could have something like, you win but you lose, the world still gets flooded but you were able to harras Ganondorf long enough that he can't escape, and the people escape to the mountain tops. I think an end where somehow(Hylian telepathy anyone, from lttp?)the hero is shown the people safe, and the water risen around Ganon's tower. And you let Ganon kill you, to pass on the hero's mantle before you are trapped in time, for if you were frozen in time the mantle would not be passed on and no hero would rise again(kinda like Obi Wan in SW4). I see a whole emotional story play out of this, there should give the character a real personality, that becomes completely heroic and sacrificail by the ending of the final battle, saving the ones he loves. As for who it is, it could be Link, an average civilian Link, not the rural boy we have come to expect. And throuought the game you would see that he is emotionaly different for the normal Links. And I think an ending seen of the people he saved mourning thier savoir. And he shall be the Hero that gave everything to save the ones he loved... Maybe the game will end on a scroll like WW began, because it was only a legend, of Zelda.
I would like to emphasize the amount of emotion should be put into this game, if it comes to form, maybe even a lovelife, yes, Zelda and him are crushing, and then she contacts him to tell him they are safe, to come to them, before he is hurt, but not wanting to risk it, Link keeps fighting, and then lets himself be killed, for other reasons as seen above. And you see Zelda leave with the royal troupe, in a ship eerily similar to the Pirate ship of WW.
Well that is my idea, what do you think?