I don't really have specific color that I use for Dr. Mario. He's my current main, and he's really the only character I ever use. I like all of Doc's palettes, and the one I use varies based on the time of day and my mood.
However, rest assured: Even though my current character loyalty is exclusive to Doc, once Mewtwo comes out I'll be maining him exclusively. Dr. Mario will be bumped down to my secondary, and some of my character loyalty will remain with him, but Mewtwo will take over as my main and a majority of my character loyalty will be transferred to him. In a game where match-ups are important, it never hurts to have a main that you're an expert with that you use most of the time, but I personally think you should also have a secondary that you're just as good with in the event that your main is hard-countered by your opponent.