A friend of mine asked me this question today, and I didn't have a solid answer. The Memory Alpha article on Starfleet uniforms (http://en.memory-alpha.org/wiki/Starfleet_uniform) states that "most of the ranking officers in Starfleet Command" wear the Command division color, namely red. There is support for this in DS9 when Worf switches to red when he takes a command position on the station. We also see Dr. Crusher wearing a red uniform when she is commanding the Pasteur in "All Good Things..." even though it is a medical ship and she is still ostensibly acting as a doctor.
We are all given command of a ship when we are promoted to Lieutenant, but the career system seems to indicate that we retain our assigned division. Concerns about how monotone the game would become aside, do you think that all players should be wearing red from the beginning because we are commanding a starship, or perhaps we should all switch to red when we hit Captain and become "ranking officers in Starfleet Command"?
I think we can easily justify admirals running around in blue or gold uniforms by saying it is just another of the changes that has been made to the Starfleet uniform regulations by 2409, I'm just interested in how people feel about this from a role-playing perspective.