>>58399511Game Freak has been worried about Pokemon being their only source of income. They actively prioritized Project Gear over 3DS Pokemon development. Ever since the GBA days, they've tried to branch out and make new IP. At that same time, Nintendo went behind Game Freak's back and poached Enix devs to develop Pokemon games for the Gamecube, as a way to boost the Gamecube's library.
That betrayal is why Game Freak distances itself from the Gamecube duology, and doesn't count them among the mainline games. In the past, we saw Nintendo iconography in Pokemon games, like the N64 cup in Stadium. TPC put a stop to that, to minimize the perception that Pokemon=Nintendo. They didn't want Nintendo to encroach. Even though GF has the most control, Nintendo projected an image of control.
GF are very cautious about outsiders having too much power. They'd rather bring Ilca in house, and form a whole new internal division with Pokemon Works, than partner with Square or Genius. They need to project the image that GF is important, and the games can't exist without them at the helm.