I get the feeling GF operates largely independently from Nintendo. They might be in the same building, but I suspect the strictly hierarchical culture in Japanese companies has lead to a situation where even if somebody at Nintendo (or even The Pokemon Company) did want to do something about GF, they'd first have to figure out how to get rid of the president (who is literally the creator of the franchise) and the current director (who's been with the company for decades). The politics of that situation seem insurmountable to me.