I don't claim other people have this problem, just me.
It is funny how small things can ruin a game, but i don't see the color issue doing that, although it certainly does eat into your playing time because you have to stuff around and waste time scrolling around to confirm who owns that little red ship on the minimap.
A good example of how to destroy a brilliant game is provided by Egosoft's X3 with the rampant collisions and freindly fire. By the time i had a nice fleet of capital ships, i was too scared to go to those sectors where my ships were because of collisions and freindly fire, it was quite absurd and i do not bother playing it anymore because of that.