Lastly, Nintendo producer Kensuke Tanabe has confirmed that Retro Studios is working on a brand new game, and it’s been in development for a few months. As for what it is, Kelbaugh won’t say much.
“We love working with Donkey Kong. It’s a great character. It’s a lot of fun. We love working with Metroid Prime, with Mario Kart; those are fun, fun games to work on. So, you know, you can’t lose,” he said. “Every one of those IPs have been a lot of fun to play with and work on and [we'd] love to come back to them sometime.”
I think this is quite significant. They've been working on a game for several months now, while they would love to "come back to Metroid, Mario Kart and Donkey Kong sometime". This basically confirms their new game is not of one of these IP's, otherwise these statements would contradict. So no Metroid Prime. It could be a new IP, it could be Star Fox. Which would be awesome.