There's one pokemon I can think of whose color has been very inconsistent over the years: bulbasaur.

He's blue. . .he's green. . .he's back to blue. . oh wait he's green again. In Go he's VERY green and could be mistaken for being shiny. I am really annoyed because he looks soooo much better with the bluer tone.

It is really interesting the color 'evolution' we've seen with Bulbasaur. I don't feel too strongly about that topic BUT I do feel strongly about the lack of vibrancy on its 3D model (and 90% of all 3D models).