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Realistically, what can Nintendo even do about GameFreak?
Game Freak is their own company and Pokemon is their own IP, so Nintendo can't really stick their nose in there if Game Freak doesn't want.
I don't know how buying the rights to the IP would work.
Cutting them off as a publisher would just be a loss for Nintendo, since Pokemon has such an enormous brand identity that, even if Nintendo kept the games from being on Nintendo consoles, Game Freak would be super well-off regardless.
The only thing I could see Nintendo being able to do to intervene is to offer to do stuff for GameFreak, like programming in all 807 G1-7 Pokemon, like how Iwata saved their ass in GS with his compression to fit KANT0000 into the game and how Nintendo got Mega Man 6 to reach North America by publishing it themselves when Capcom wouldn't.