I think developers should rid the world of Gohma and Dodongo. I know they're classic, and we've fought them many times with many different strategies, (though they're weaknessess are the same), but they are getting kind of old.
Another thing I want gone is Hyrule Catle. Allow me to explain. I want a game where Ganon becomes powerfull enough that he actually destroys Hyrule Castle. Like, in the beginning of the game have Link go see Zelda somehow in the Castle, and then after a few dungeons of Ganon/dorf raid it with an army of his minions and completely destroy it and leave it in utter ruin. And then not build his base in The Castle area, have it somewhere else. I think this would make the story much more interesting.
Lastly, I want them to leave out other Realms, and instead make Hyrule bigger. One of the things I liked about TP was that even though they had the Twilight Realm, they didn't reuse dungeons in the Overworld as dungeons in the TR. I didn't enjoy the small world in aLttP, and I won't enjoy it in Zelda Wii.