aquisitions in Japan are definitely tough to pull off if I remember correctly
Nintendo's best candidates for aqcuisition are:
+Next Level Games - the only independent studio that Nintendo trusts with ip such as luigi's mansion, mario strikers, and punch out. It surprises me that they are not first party.
+Shin'en - Strong supporter of Nintendo through thick and thin. Their games also have high level of quality for an indie studio (not AAA, but excellent nonetheless)
+Koei Techmo - Definitely an interesting choice. Not a developer that has done anything ground breaking, but they definitely have potential to break out solid titles, and with a proper lead, they could truly grow to be a great asset
+Level 5 studios - Although I don't see this one happening, given level 5's great commitment and success on the 3ds, acquiring level 5 could lead to better and consistent support for handheld games
Unlikely to happen:
-Platinum - They seem glad to transition between consoles and probably won't be limiting themselves to an acquisition anytime soon.
-Capcom/sega - They are still to big to be acquired. Nintendo already tried to acquire more out of Namco Bandai, but all they could manage was the monolith soft team (great acquisition btw). Perhaps Nintendo could do something similar for Atlus with Sega, but I doubt this greatly