I don't know how they decide everything else but the hero (Hikaru) of the story almost always get the mostly red/sometimes white/blue w yellow accents combo (superman, optimus prime, etc)
Roy gets the dark brooding colors, max gets the cooler colors and of course kakizaki gets the CF colors.
But it's mostly done to make the character recognizable and not a military scheme type thing just like the stripes on the valks don't really mean anything.