If you want my honest opinion, and not just me regurgitating things I plainly don't care about...
I'd think it's Atlus.
I wouldn't care about Sega - at all - if Atlus wasn't under their care. They could very well guide Sega to a better future in terms of software development and localization.
A close second would be Monolith Soft, if they developed titles faster, that is. Their philosophy is actually really compatible with Nintendo - especially with the top brass - and I think they could very well guide Nintendo to a brighter future. They're already working with third-parties like Bandai Namco (though only PxZ has come of it...they should do more, like Xenosaga HD collection?), assisting other first-party studios (see their assistance with The Legend of Zelda for Wii U), and they've blazed forth with a new genre and lead IP for Nintendo (open-world RPGs, and Xenoblade).
Though, I'd be inclined to agree and regurgitate what others have said in this thread.
I WON A BET AGAINST AZUREN! WOOOOOOOOOOAAAAAAAAHHHHHHHHHHHHHHHHHHH
:3
