Barring any crazy steampunk Retro-Zelda, the two clear options to me are Prime 4 or DKCR2. Honestly, I'd be happy with either (and it's possible that they could be making both). The Prime mechanics have some real possibilities with the Gamepad. Moreso than 2D Metroid, I'm sorry to say (but not TOO sorry, since I want to see that on 3DS with parallax scrolling). And I'm sure DKCR2 would be a super-solid game, especially if they took out the few annoying features of DKCR (you know which ones).
Yeah that's an obvious one and it might be fun to see them do something new, but I don't want Metroid to be dead, and I don't a follow up to Other M... or do I? I don't know, I'd like to see them go back to that cinematic storytelling but just get it right with a better story and voice acting this time.
For DKCR2, I hope that's on 3DS, maybe Retro could make that too? Why not! Lot's of studios transition from 1 to 2 games.
Because every time I put faith that a new Metroid game will appear (see Metroid Dread), it doesn't happen. I really, really want it to be Metroid Prime 4 though and it would be perfect for the controller But one thing though... if there's a lot of focus on the new controller, would they work in Wiimote controls as well? Part of what made the trilogy so awesome is the ability to replay the first two games with the upgraded controls. I don't want to sacrifice that and have to use a dual analog setup. Though with the recent confirmation that we can use the classic controller in combination with the Gamepad, I'm sure they could make it work. It just means we have a lot to work with then
I think if it was Donkey Kong we would know about it by now, I think they held off telling us at E3 because they wanted something at E3 2013 to rival the other console announcements. I do think its Metroid Prime 4 but it could be Starfox or maybe F-Zero. I just don't think DKCR 2 is going to cut it as a megaton announcement.