Frankly uniform color doesn't bother me to much as there are so many different vintages running around the game...it is nice to see someone pick a color other than red especially if it agrees with their specialty...with star fleet now allowing all these admirals it is nice to see their background. In other words as the game already disagrees with canon on numbers of admirals then I think color helping to differentiate types is a good compromise for now. Otherwise, almost everyone in the game would be wearing gold(TOS) or red(TNG-on) once they reached Captain.
My pet peeve is with people openly wearing kits instead of hiding them when they are not on a mission. Don't get me wrong, people definitely have the right to dress how they want but I just think it's odd to see commandos with backpacks everywhere, even though we are at war...game NPCs are guilty of this as well. This is earth space doc...not mos eisley. Leave the battle wear and showing off to the KDF in port. I grant exception to the the STF office on DS9...it just seems more logical there. Anyway just minor peeve of mine.
I wish that there was an option to wear armor in missions and in pure social areas remove it automatically. It's a pretty low priority, though, I'm sure, and I'd rather the devs fry bigger fish.
Most of the time when I'm in full combat gear in ESD it's because I forgot/am too lazy to muck around with the visuals. It's a bit more jarring for me to beam down in a combat zone with my First Contact/Dominion War-era uniform as opposed to battle gear.
Actually I kind of wish there was a more uniform uniform. I'm glad to see all the variety, but one (or a few) "base models" would be helpful, IMO, preferably preset costumes so you can just grab one. If I recall correctly there didn't seem to be anything like that at chargen.
I use the Wrat of Kahn color where the Captain has white as command. My lib borg first office uses green as XO, a homage to kirk's green tunic, and borg primary color. Everyone else uses the standard color of red, gold and blue.