Would it ever be possible to involve a feature or sidemod that very slightly adjusts the hue/saturation/brightness at random for each individual Pokémon so that every one has a unique coloration? You can see the concept in action in this rom hack.
And below is the initial concept visualizer I made. The bulbasaurs are playing with changing each color range individually but I know that'd be far more difficult so ignore that; was just an experiment.
I think it'd make a fantastic encouragement to more carefully choose the Pokemon you catch and make it feel more like your own, not to mention encourage you to catch more Pokémon in general if not just cause they look interesting! Lastly, it'd help break up the monotony of grinding just a little bit. I see it as similar to the size variations. Those alone have been reasons for my friends and I to catch certain Pokémon, I think it's an awesome feature.
There is the issue with some existing shinies being alterations of the base palette but I actually think that could make it more fun; a little harder to know for sure until you see the sparkles! Once again encouraging more interactions with the Pokémon around you.
This is an absolute dream feature of mine and I adore it so much that heck I'd be willing to pay for someone to whip up a sidemod with it if it's possible! I'd highly consider up to $50 though I'm not a programmer so if that's a total lowball do let me know; very willing to barter.
Thank you so much, have a lovely day! :)