Because Game Freak is only part owner of Pokemon. They split it with Nintendo, Creatures Inc., and I'm sure The Pokemon Company (joint business between the three) takes a cut too.
It must suck to basically be stuck working in an environment you're not really good at. 3D is complicated just from an art/animation perspective, so I can sympathize with that.
Though if Pokemon prints money, why is Game Freak still so small and having these problems hurt them?
To be fair, they made other game these past few years. Screw Breaker, Giga Wrecker, Rythm Hunter, Little Town Hero...
We tend to forget them because in our mind Game Freak = Pokemon and as soon as they do something else it is shadowed.
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