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GameFreak's arguably more protective of Pokemon than Nintendo is about Mario, and for very good reason.
They have a literal money-printer that'll shit out cash no matter what they do. Games? A million guaranteed. Movies? Very nice box office returns. Merchandise? YOU BETTER BELIEVE IT'S PROFITABLE.
They don't trust anyone but themselves or TPC(i) to handle any serious mainline involvement with the series, and only consider experimenting in other genres via spinoffs.
In Amiibo's Case, they don't really see a point to make them useful and profitable. Mythical Pokemon? Movies in Japan already have that covered. Free Pokemon like starters? Nigga, you can just use the GTS for that. Free Items? Absolutely worthless and better off being used in Demos or Pre-Order Bonuses.