The studios that Nintendo has bought over the years that have worked out the best were small developers that had a lot of talent but were unable to be particularly successful for a variety of reasons. While I’m certain that we could possibly name of a handful of studios (Platinum Games) most of the studios which would make the most sense are unlikely to be on anyone’s list.
If I was Nintendo the approach I would take would be to look at the top independent talent producing games for the iPhone and try to aquire as much of that talent as possible (either through recruitment or buying the studios) with the goal of adding 12 to 24 development teams that are able to reliably produce interesting games for their next handheld; ultimately, this would probably end up being less expensive than buying a couple of established studios. From there I would take several of the best teams that were focused on DS games and consolidate the teams and recruit the (countless) developers that have been laid off by other studios and have these studios focus on games which are (roughly) the level of Wii games; and they would continue developing games with a similar scope even on Nintendo’s next generation hardware. After that I would focus on taking the best Wii studios and recruiting as much knowledge from studios that already focused heavily on HD and get these developers ready for next generation development.
Ultimately, you could say my approach was to find talented small studios and over time to consolidate their talent and augment it with outside people to have as many of the best studios in house over time.