I don't know if color matters in a competitive standpoint. Perhaps it's all a mental thing. For me, though, I am very particular about my colors:
R.O.B.
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Pink: Pink and purple are my favorite colors, so this is the only one I go with.
U.S.A.: I only go with this grey color if my opponent becomes a douche king and steals the pink. XD
Peach
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White: Let's face it, a girl's gotta look her best while dishing out an ***-whoopage.
Red: Though rarely used, I think she looks good in red. Also reminds me a little bit of Lydia during the wedding in the movie, Beetlejuice.
Ganondorf
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White hair: He looks ******, especially with the ancient look. As everyone knows, ancient/old guys who can pwn are always awesome... that's my opinion
Red: Chosen if my opponent steals the white colors.
King Dedede
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Pink: See R.O.B..
Purple: If pink is taken.
Meta Knight
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Pink: Although I almost never use him, when I do, I always go with this color, since the color scheme with the reds and yellows reminds me of Kefka Palazzo of Final Fantasy VI (see my avatar). If someone else takes this color, I simply don't choose Meta Knight.
That's about it. There are other colors, but they're to characters I almost never play. I only mentioned Meta Knight for the Kefka reference. XD