I'd love to see the Light theme fans have been anticipating since the release of OOT. How it would work with the 3D technology though, I don't know. An electricity themed dungeon would be a really neat idea, and could really work well in 3D (imagine lightning coming out at you!). I'd also like to see, not an ice dungeon, but a frozen water dungeon! I love the idea of revisiting dungeons, and a water dungeon is the perfect candidate. Complete it while it's thawed, come back later to find it frozen, with completely different puzzles thrown out at you. It would be the same dungeon, but a different dungeon at the same time!
I would also like to see (though I find it highly unlikely) an actual 3D based dungeon (kind of like the color dungeon from LADX). Not called "3D temple" or anything, but just a dungeon in which you actually have to use the 3D to solve puzzles! For instance, imagine a puzzle where you had to figure out which object is nearest you? Or an enemy that you have to use the 3D to decipher just how close his weapon is to you, and then move accordingly!
Just some ideas I decided to throw out there...