Some additional thoughts on this subject:
1. I'd like to see a system in which admirals can issue two kinds of strategic commands: general patrol orders to groups of ships (fleets) under their command, and specific strategic missions to individual ships. ("Captain, we need to build a tactical starbase in the Taglar system of Sector 21, but the Taglari don't trust us enough yet. Go find a way to gain their cooperation.")
In both cases, I'd hope that both admirals and captains gain something from the exchange. If giving and following orders are just things you "have" to do, then there'll be less incentive to follow orders. In the real world there are ways to deal with that; in a game, not so much.
This is why I advocate a system whereby admirals have to put some of their personal prestige on the line to give missions. If the mission fails, that prestige is lost; if the mission is successful, the admiral gets that prestige back plus interest (and the captain and crew gain mission prestige). This way there's a reason for admirals and ship captains to want to work together.
2. What capabilities are needed in order to be a good admiral in a MMORPG? I'm not sure we can speak to player abilities, but we can talk about what abilities might be required for a player's character in order to successfully navigate rules-based gameplay.
What about the idea of requiring the character to have learned certain skills in order to be eligible for promotion to some ranks?
With respect to admirals, necessary skills might be Fleet Operations, Advanced Logistics, Military-Civilian Relations (i.e., politics), and Long-Range Planning. The more skills like these you choose to learn, the better your odds of winning promotion to flag rank.
Of course, this assumes that Star Trek Online will be designed so that skills can be acquired independently of rank. If instead ST:O follows the usual MMORPG pattern of only giving your character whatever new skills the developers think you should get when you magically gain a new "character level," then presumably there'll be some other mechanism for achieving promotion to Admiral.
I'm hoping it's more than just, "Congratulations, you've ground out 1,000,000,000 prestige points! Would you like to buy Admiral rank now?"