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I can see them introducing it in a way where it's bad at first.
Like the new bad guy team or a team of scientists similar to the Aether Foundation create powerful Pokemon fusions for the purpose of creating the ultimate race of weapons and sell them to terrorists, dictators and other baddies for a profit but they initially present themselves as a team or researchers aiming to understand Pokemon better and they trick the protagonist into catching certain Pokemon for them.
Once the gig is up, you and the other protagonists introduce basically rescue the fusions who are treated awfully and you can use them in battle but there is a catch, they completely disrespect your authority and either loaf around or use their own attacks no matter how many badges you have and the only way for them to respect you as their trainer is to treat them nicely by feeding and petting them in Pokemon Aime and such.
I wouldn't mind seeing this, especially if the fusions themselves look cool.
