Don't know if this has been suggested (or shot down) but I'll suggest it anyways.

Anyways, I think it would be a neat feature if you could pick and choose what skybox appears. The way this could be done is in the game settings menu. Simply enable which skyboxes you want to appear in your next game. Could be useful if you dislike a certain skybox and it always seems to appear or you simply want a certain one to appear, as it is pleasing to your eyes. Yes I know that there is an option for enabling/disabling colored and deep space skyboxes, though that doesn't narrow it down much.

Just a suggestion, don't know if its too late or not or if this can be done via mod.