I love color coding characters. I think it’s a fun tool that is very hard to get right, and often doesn’t have a place in most movies, but Sky High uses their color coding masterfully, and I can never stop thinking about it.
First, there’s the basic reason they all have a color: Superheroes have set colors/color schemes. Its one of the most important things about them, and when characters go through costume redesigns, they typically have the same color scheme.
Second, each color scheme reflects the characters personally:
Will wears red, white, and blue. Yes, yes, he’s the all American kid, but it reflects something deeper. As @darrenpeace pointed out, Jetstream used to wear gold, teal, and white, but changed once she married The Commander. Mr. Boy wore red, white, and blue when he was All-American Boy. Will wears red, white, and blue not for himself, but to impress his father, and be the son he wants him to be.
Gwen wears pink, but only when she’s trying to be the perfect girl for Will, and what better way than to wear the most feminine color? When she’s Royal Pain, the accents on her outfit are yellow: the color of deception.
Layla wears green, not only to reflect her plant based powers, but her own passion for the environment, and at times, the jealousy she feels towards Gwen Grayson.
Warren Peace wears colors not reflective of his powers, but instead his demeanor. He is tough and grizzled, which is why he wears black leather. At times, he wears red, but flames are generally depicted as orange or yellow.
Zach is my favorite, honestly. He wears neon clothes all the time, which are reflective(haha) of his powers, but also his confidence. His clothes draw attention to himself, since he is in no way insecure. He loves his powers, trusts them, even if they aren’t the most practical.
Magenta is purple/well… you guessed it. She’s edgy, alternative. She doesn’t wear pink, which is expected of girls. She wears magenta, which is a darker version of pink, to highlight a mixture of femininity and punk.