I know that this is not a high priority feature, and probably was already mentioned, but it would be nice to have option to choose different color schemes for ships ingame. This
http://fractalsoftworks.com/forum/index.php?topic=3491.msg111882#msg111882 thread made me remeber this idea. So basically we will have in refit screen option to choose color scheme of ships. It would be even more cool, if it's possible to implement basic color adjustments in refit screen(for example like in any racing game it is possible to choose colors of main parts of your car), or even place some marks/small pictures or faction emblems on ships. Shields appearance customization?
Anyway, when the time comes, it would be nice to have some sort of appearance customization for your ships. Imagine that your specially designed missile frigates not only have distinct role on the battlefield, but also have distinct color scheme.
P.s. Also, because I already made too many threads, I will post this little suggestion about 0.6a here. I think that those red marks indicating such things as not CR ships are too similiar in appearance. Also you can't see smaller ships behind these marks.
And there is a little problem with post combat dialogue screen. I think that there is not enough distinction, especially visual(thus easier to handle in a long run), between alive/destroyed ships. Of course it is not hard to see, but something more eye-catching would be nice, also that your fleet, enemy fleet, retreated ships etc. - everything is packed to tight in one dialogue without very distinct visual marks.