Well it's very minor and I probably missed the train already but one of the things I would like to see is ability to use player's own logos.
Just an image (.png, .jpg,.bmp ...) you could load when starting a game that will appear on all your screens (and hopely ships) in game instead of default race logo.
I believe it's easy to implement and will add some very positive "feeling" into a game , such small things make an "athmosphere"