Add more ship paints.
Additionally two look presets would be welcome. So, for example, players could switch between them if they wanted two different looks for red and blue. But this would require some actual work from muse guys.
I'd like them to do it like they do the team color paints in Team Fortress 2. It keeps blue team blue and red team red, but has a variety of shades that apply to each ship. So, light blue on a blue team ship is light red on a red team ship. Dark red on a red ship is dark blue on a blue ship. It's quite clever.
Perhaps purple and orange could be "red team" colors and green and yellow could be "blue team" colors. I just want easy visual identification while maintaining variety. And I suppose some paints could be universal (black, white).
Muse long ago admitted allowing blue ships to be painted red and red ships to be painted blue was a dumb move. I wish they'd retread this idea and overhaul the system.