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.

We've talked about this before. The uniform priority goes with color matching of the person. Here's the list in priority order:

Blue eyed folks wear Blue
Blondes/yellow eyes/yellow visors wear Yellow
Everyone else gets Red

And Wesley and toucans get a rainbow. :p

Looks like I have answered my own question: http://www.stowiki.org/Grigori_Yanishev
An in game admiral wearing something other than red. So, I guess it is up to every player to decide if they want to join Starfleet Command at any point during their career, or stick with whatever division they came up in.

Generally speaking based on the show's division specific coloration can be designated in the following way:

* Command & Tactical Red
- for any "flag" ship (if you are carrying the UFP flag on your hull)
- Any and all Tactical officers

* Operations & Security Gold
- Tugs, engineering support craft
- Refit & Repair Starbase (eg: utopia etc.)
- Transport & Freight ships
- Planetary & System Security patrol ships/shuttles

* Science & Medical Blue/Teal
- non combat Science ship
- Non combat survey ship
- Medical support craft (but oddly not hospital ships)

* Flag officer White
- Captains dress uniform
- Admiralty command uniform (though some still wear red with white highlights)

From what i can see in Memory Alpha and Memory Beta it appears to come under the simple heading of if you are a ships Captain it is expected for you to wear Command Red but below the rank of Lt Commander you generally stick to your division colour regardless of your current command role, the only real exception to this was Lt.Commander Worfs switch from gold to red but in that case he switched from Head of Security (gold) to a Tactical and operations officer (Red) which does stick to known canon.
The entire Admiralty on the other hand has the choice to pretty much wear what they want to but its seems to be primarily dependant on there role at any given time eg: the Admiral in charge research and development on Utopia Planitia can wear red as a flag office or white as an Admiral or simply wear gold if his prior specialty was in engineering.

I hope this helps it did take a little research but anything to help the immersion factor is a good thing.

Of course if you like the proper original TOS color schemes, it's

Command/Operations: Gold
Engineering/Security: Red (hence the term 'Redfshirt')
Science/Medical: Blue

While there is no stated evidence that I am aware of, I believe the uniforms in the STO universe have completely eliminated the command color distinction. In this timeline, red represents security and tactical, not command.

To your question about RP, I think it makes more sense this way. In a time of war or emergency, it's better to designate uniforms based on skills and specialty so leaders or people not familiar with your face can designate assignments to you accurately.

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.

THIS.
Like you said, I think that this is a game and people can do whatever they want to have fun while playing it. But personally, I don't see the point of wearing your "kit" (or worse those hideous armors) when you are on your ship or walking around Federation controlled stations/bases.

I just wear black all the time because all the episode content in STO always involves away team commando missions.

Red is not a good colour choice when ambushing Klingons because it just shouts SNIPER AIM HERE

Given how there is no single uniform regulation, colors mean nothing. If this were actual Starfleet, all personnel would have to wear the same uniform (so no uniforms from the different series). But since this is not the case in STO, color coding is moot.