If Nintendo bought a studio I think it'd have to be one that bolstered their games selection into genres Nintendo has traditionally not covered. I think everyone's already mentioned the main Japanese favourites, so maybe:
Obsidian: WRPG developer that could make fantastic games with a lil' Nintendo input
Insomniac: They may have a strong relationship with Sony, but they also have experience with multiple genres and have a strong history of console development.