Vanpool. They're the guys and gals who made the Tingle RPG on DS (a real gem, not being sarcastic), and Dillon's Rolling Western on the 3DS eshop, among having contributed on other stuff like Little King's Story, WiiPlay Motion and Mario & Luigi on GBA. I'm thinking they could become a real great dev under Nintendo, and they have a really quirky and unique vision of how to make fun and interesting games.
Shin'en would be a good bet too, though they're currently already practically a Nintendo 2nd party anyway. :p They're consistenly putting out quality stuff for Nintendo's platforms.
Vigil might be a good one as well. They could very well become something like Retro, under Nintendo. Clearly they have (had) some very talented people and interesting ideas. They seem really fond of Nintendo, too.
As others have suggested, HVS would make an interesting candidate too. I think as an independent dev they're really struggling to turn their visions and ideas (which seem to be great) into full games, having to deal with very limited budgets and deadlines, as well as lacking a publisher. Nintendo owning them could really help them out a lot, I should think. Them being really devoted to and excited by Nintendo themselves would seem like a plus, too.