I'd like to see a Dark Link battle as extremely challenging as AoL's Dark Link battle if not even harder. An epic sword-on-sword battle with yourself ... sounds intense! They should make it where all your weapons are disabled other than your sword and at the point you fight him, you can only possibly have one sword, the sword Dark Link has as well making the battle extraordinarily challenging, the type of battle I want!
An enemy that was 2D in its only appearance that I think would be cool to see is Manhandla. That would probably be my all time favorite boss if they got Manhandla 3D. I have no idea how the battle would work, probably trying to sever his for claws while they snap at you or throw things at you. Probably once they're gone you'll have to attack the center where possibly and eye is (as with most other typical Zelda bosses) and it would be defeated. Seriously, that would be epic.
Gyorg is one of my all time favorite bosses because I actually died while battling him. A few times. His battle was extremely challenging, and if they brought him back with even more challenges, I would be one happy kid.
Thunderbird is a very unique boss. I'd love to see him again, although I would have no idea how the battle would work.
Helmasaur is probably my all time favorite 2D boss battle because it was just so awesome. If they were to get a giant Helmasaur in 3D, that would probably be a pretty hard and pretty cool fight!