Are you using Colored Skyboxes ?
I suppose Colored Skyboxes were added for their potential "wow" factor and that they help units visually stand out against the background, but I personally can't stand them. I bought this game as a space strategy game. Space is pitch black and dotted with stars, not lime green with dense clouds or sky blue with a white horizon. It's just way too implausible.
Some comparison screenshots :
Normal space color:
http://img17.imageshack.us/my.php?image=screenshot7la4.jpg
Various colored skyboxes:
http://img17.imageshack.us/my.php?image=screenshot6uo4.jpg
