The smartest move would be a new IP. Sure they revived Metroid and DKC and their name is Retro, but if Nintendo wants to start new IPs (that stick) I think Retro has the backing to do it.

A new IP is never wrong, except if its a bad one which was very often the case lately :/
A new Starfox game would be also very cool.

I would like to see Retro make ALL of the following for the Wii U:
Completely new IP
New Metroid Game
New Zelda Game
Why limit them to just one? They will not all be released at the same time, but over 3-4 years, this should be possible for them. I would especially like to see what they could do with a Zelda game. That series really needs a re-boot to make it fresh again, and Retro is great at that sort of thing.

Anything they do will be worth a purchase, but I'd love them to make a 3D Donkey Kong. I loved DK64 and Retro could do incredible things with it.

I completely agree with you.

I'd like them to come up with a new IP. They've handled Metroid and Donkey Kong, and they had some involvement in Mario Kart 7, so now it's time for them to shine on their own.

I'd like it to be some kind of big adventure game, something with a huge world to explore (but without too much backtracking). If it were to be some kind of FPS game, then I'd hope it was more like BioShock or Metroid Prime, rather than a straight FPS.

From 3:45 onwards: All rights, including copyrights... bla, bla, bla... reserved by Nintendo.

I'd love to see a new IP. Given Miyamoto's recent comments about F Zero, I don't think an F Zero game is in the works anywhere at Nintendo, but might appear in the next few years.

If it's not a new IP, Starfox or Metroid are quite likely. I agree with others, though; the launch of Wii U is a great time to launch a new first party IP and give it maximum exposure. 

EDIT: I'd like to see Retro co-develop the next Zelda after their launch title, really, and assuming that doesn't take a ridiculous amount of time, then return to Metroid or resurrecting an old IP.

I'm happy to leave F-Zero to Sega, they did an awesome job with GX and I feel Retro's strength at creating a believable and cohesive world would be somewhat wasted on F-Zero. Although I'm still not sold on Retro and Zelda the thought intrigues me. Preference-wise I would love to love to see them tackle either a new IP or a new Metroid and I also feel these are the most likely options.

What I don't want to see a Metroid/Starfox crossover, I just can't see it working. The only way I can imagine it is where Starfox and friends and drawn into the Metroid universe with a more 'realistic' twist e.g.. they are part of some race that is composed of human/animal genetic hybrids or something along those lines. My least favourite of all the options though.