If I had to pick one, I'd choose a 2D Metroid. Metroid needs a game to regain its footing, and a 2D Metroid on the 3DS (somewhat ironic) and Wii U would be a fantastic way of doing so, particularly something that finally deals with Fusion's stupid 12 year old cliffhanger. Can't imagine it would be particularly hard to put it on both systems either.
When it finally does return to 3D, I'd honestly prefer another stab at 3rd person. The Prime series is utterly fantastic, but I get the sense that Retro did nearly everything there was to be done with a first person Metroid. If it has to be first person, don't make it Prime 4. Make it a Prime style game set somewhere else in the timeline; or, even better, a Prime style game controlling a new character.
A 3rd person Metroid, meanwhile, has been nowhere near fully explored, and given a full control scheme to work with, as well as a return to exploration and a not insipid story, could be something fantastic.
