I've heard this rumor on wiiudaily, nintendolife, gamefaqs, etc, and while none of them seem like a credible whistle blower, the possibility rather scares me, epecially since their work on Mario Kart 7 does set a precedent for it.
Retro is one of the most talented developers in the world in my view; and they have a very different vibe to other Nintendo teams, allowing them to do things you'd never see from, say, Tokyo and Kyoto EAD, like Metroid Prime.
To waste that on something any of Nintendo's studios could easily make would be more disappointing than Resident Evil 5 and Metroid Other M put together for me.
Not to mention Nintendo desperately needs a visually stunning "core" game like Prime on Wii U, which Retro would be perfect for.