please realize that I'm assuming that in
OoT link beats Ganondorf and hands him to the sages and they try to kill him but instead he gets pulled into the twilight then comes
TP and link wounds him and them after some complex interesting weird still to be explained in a future Zelda game stuff, the land gets flooded with water becoming the great sea, then comes WW and finally
PH.
Phantom Gannon isn't dead yet, so he's still able to do his evilness also if there's a Phantom Gannon and dark link then there must be a dark/phantom Zelda. The Gorons and Zoras would pop back up to
Here's my idea for the story
Link is sailing the great sea with Tetra , when his ship is attacked by evil minions

, and somehow after some fighting Link goes through A mirror that opened up into a portal, as you've probably guessed Link is now in the dark world and he ends up as a very strange animal that by your choice is either a wolf, tiger, or bear.
The rest of the game would revolve around switching between worlds(Using the mirror from LttP) and clearing different dungeons.
I haven't cleared much up about things, except for the general story, because I don't really have the time, and they're not going to do a complete make of some random idea.
And here's the other things.
There'd be different armors like the Goron's armor(Like the power bracelets),Zora's armor(Allows you to swim), and the Rito armor(Allows you to fly like in WW when playing as that little Rito girl).
And maybe if they couldn't decide between cartoon or realistic, they could just make a cartoon version and a realistic version.