Just a thought: don't make ship colors faction-based. Instead, let every class of ship have its own color scheme available. For example, make a large, obvious, brightly-lit flagship to proudly carry the standard of your civilization forth into the unknown. However, for more clandestine, belligerent purposes, a black/gunmetal color for stealthy ships would be more apropos. I know it would require some big tweaking, but just a thought. Feedback?