my personal best guess is star fox i don't think they are working on a new metorid due to the fact that the prime series is pretty over

I think it's working on two projects.

I think the four most likely suspects are:

Metroid (not part of the Prime series)
Star Fox reboot
Donkey Kong Country Returns sequel
New IP

I'd guess it is a game for mature audiences like an FPS or adventure game, maybe a new IP.

I'm really hoping for a new IP. A western RPG made by retro (skyrim style) would be awesome (and a really good system seller).

I voted a DK game. How long have they been working on it?

A new RPG!

I think it's a new IP

I was kind of hoping that they were working on Eternal Darkness 2, but that was admittedly a bit of a pipe dream. With Shadow of the Eternals having a planned Wii U release, Nintendo knew of its existence before sending Dyack and company a dev kit, so that pretty much rules out ED2.

Considering the talent Retro has hired in the recent past (2011-August or so last year), I could easily see them working on another Metroid. It wouldn't be Prime 4 because even with the cliffhanger on 3, everything related to the Metroid Prime has been taken care of. Dark Samus was born of the Prime, her Phazon Suit, and the Phazon itself...and she was delt with. It could very well be Metroid Dread....possibly re-tooled to be first person like the Prime Trilogy as it was rumored to be a 2D game, set after the events of Fusion. The Japanese have this superstition about the number 4 too....

Their hires were mainly artists and animators....people from Naughty Dog (enviro artist for U3), Bioware (animator), Junction Point (lead character designer from Epic Mickey I believe), 2 or 3 people from Vigil (contract artist and character designer from Darksiders 2), 2 from Red Fly (Cinematics, worked on Wii Force Unleashed 2), Gearbox (enviro art lead from Borderlands 1), a couple of interns that worked at Viceral while Dead Space was in development, and this guy: http://www.linkedin.com/in/kbtaylor?trk=pub-pbmap  that summary....hella experience.

The contract artist from Vigil, drew this...while not paying attention in class (I would embed, but I don't want my post to be any more massive than it has to be) http://fc09.deviantart.net/fs7/i/2005/235/a/b/Yarrarg_by_reflectingabyss.jpg 

They also hired another artist who drew this: http://fc01.deviantart.net/fs71/f/2011/023/f/c/a_is_for____by_beastofoblivion-d37u8g9.jpg

I'm pretty sure it's not Star Fox, haha. I think they should let Kamiya make Star Fox since it is his dream project and it would be phenomenal. If it is Metroid...awesome..I love Metroid. If it is a new IP....also awesome considering the talent they've got. ED2 would baffle me at this point, and I am having a hard time coming up with anything else that would use that kind of talent. Whatever Retro is working on though, it is going to be badass. That's for sure. 

F-Zero

Im predicting two game simultaneously being developed
1: Metroid
2. Starfox