I don't know, I feel like GameFreak have the leverage here, because if Nintendo don't cooperate then they can find a way to cancel the contracts and go release Pokémon on Sony systems or something. Pokémon has such a huge fanbase that I would think most people will go where the games are, so I think Nintendo have more to benefit from the partnership than GameFreak, at least now that Pokémon is so successful and established.
Then again, that may not be possible depending on how the partnership is set up. I don't think we'll ever know exactly how it works, but the bottom line is that Pokémon is not completely Nintendo.