I'm with Morphy. A variant that I've seen work well is: the vast majority of the pets are "normal" colored (Jolteon is yellow and white, for example) Some are "shiny" (adhering to whatever colors the "shiny' version of the pokemon is) and then, eeeevery once in a blue moon, some turn up with a minor variation- like a standard-issue glaceon with, I don't know, green stripes. Nothing alarming, just enough to add a leetle variation.
But of course, more complexity means more bookkeeping for you. Honestly, I think adhering to the standard color palette can be very rewarding- it's amazing the variations to a theme colorists can come up with when they have to.
((Also, if you need it, I will color for joo.))
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