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Not sure if its what you're looking for, but Stadium and Stadium 2 did something similar. There's in-game code that allows for massive color differences (pic related: these are two non-Shiny Venusaur but they look incredibly different) but usually its a lot more subtle. I'd love to see it implemented back in the series because it'd be a great way to help make Pokemon feel more distinct one another, like how LA/SV had differing sizes for Pokemon.
