Those of you who have played The Legend of Zelda: The Minish Cap might be familiar with the story that is told when you start a new game.
A Long, Long time ago, when Hyrule was about to be consumed by darkness, the tiny Picori descended from the sky, and bestowed upon a young boy dressed in green the Picori Sword and a shining golden light. With wisdom and courage, the young hero drove out the darkness. Now, every 100 years the Picori return to Hyrule, to provide humans with magical gifts.
The game with that story (not Minish Cap) hasn't been made yet. Link is supposed to NOT wear a cap, the Picori Sword (4-Sword) must be the ultimate sword and these enemies (among others) must appear: Moblins and Octoroks. Since this game takes place before Minish Cap, Vaati cannot be the bad guy here, because he isn't born yet (or something).
Then there is the struggle about the time-line... some claims that Minish Cap is before Ocarina of Time (if that's the case, then Ganon can't appear either)... If Minish Cap is after Ocarina of Time, then you can use Ganon as you wish... When the game takes place is up to you, as long as it takes place before Minish Cap.
Anyone who wishes to do a Zelda-game but does not know what the story will be, then I'll give away this one!