Sometimes I colour co-ordinate, but other times a lore scheme could work quite well.
For example, I'm going to be looking into running team parasite where Eliza #7, Filia/Squigly #16 is a good scheme because of Eliza's dominance over the other two - the same principle could be applied by making Eliza the odd colour, in either complementary (Squigly/Filia 3, Eliza 2) or harmonious form (i.e. Eliza 21 with Filia 13 and Squigly 11 or15).
I also like Filia 8/Squigly 16 because it makes for a nice black/white contrast, adding Painwheel 4 or a kinda bad team.