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NPC pokemon should have the same 1 in ~4000 chance to be shiny that wild pokemon have, just for funsies. Maybe give a higher chance to the NPC's whos job makes sense to maybe grind/farm shinies, like breeders or pokemaniacs or whatever.
If we ever get a canonical global grand champion character who's supposed to be stronger/higher ranked than even the regional champions, their ace pokemon should be shiny, whatever it is. I can't think of any character who could have a shiny pokemon and not have it just be cringe. And I say this as someone who majorly simps for multiple characters.
Pic unrelated