How about, we start from scratch.
We recreate Hyrule or Termina or better yet we create our own land. It's a new Link, new Zelda, new villain. We create new weapons. We give it a new story, not a OMG save the princess. But something more. That's my first proposal.
Ooooh, maybe something where we get to control Ganon for once? Or Zelda?
For the controlling Zelda one, I'm having two ideas. One is kind of taking TAL's idea, and we are Zelda during the seven years Link is gone, as she's hiding from Ganon, learning Sheikah magic, and maybe protecting her citizens. The game would start when OoT starts, and end when OoT ends, but the focus of the game would be during the seven years, and the part prior would be like the Lost Woods was to Link.
Second control-Zelda idea: There's a prophecy from someone (Sheikah, or maybe the stars, or maybe handed down in the Hyrule Royal family, etc) that a great evil is coming (not necessarily Ganon, but it could be), and that she needs to A) prepare the nation for it (hiding various keys to the Master Sword or or Temple of Time or whatever in dungeons, etc) B) prepare the nation for the arrival of the prophesied hero C) find the hero and D) teach and assist the hero.
As for controlling Ganon, I have a lot of ideas in my head. We could have elements of RTS games as Ganon raises his army for battle against Hyrule. Or elements of FPS games where there are a lot of huge battles to be fought, and key points to be captured. But if we were to go with the control-Ganon idea, I would like it to have some incredible army battles. Or even navy battles (if we decide to give Hyrule an ocean or something, similar to Termina).
EDIT: As for the bosses without dungeons (which I love the idea of), WW kind of had that with the Big Octos, PH had the idea with the monsters that protected the islands, and ST had the idea with the Rocktites, and I'm sure there are more, except those were rather easy to beat. I like the idea though, except we wouldn't just have random clones of one boss lying around the map randomly. They would be actual bosses, with the same kind of individuality that the others have (oxymoron, haha).
Also, seeing as bosses are so cool, I think in the main town there should be a fortune teller that gives you the option of letting her hypnotize you and have you remember some of your greatest fears/enemies/whatever we want to call it, and then you'd basically go into a boss battle mode. We could have the options as allowing you to choose which boss battles you want individually, or do a complete run. Maybe we could have it so that you unlock the battles by going on sidequests (obviously the sidequests would come after the boss has been beaten already in the dungeon or wherever), or we could just have it be unlocked immediately upon defeating the boss (kind of lame, because you have less replay value).
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