As Admirals, normally you would have a serving Captain under you to manage the ship whilst you tasked yourself with more management issues than anything else. So as a flag officer, why not introduce a new tier of skills for BOFFs and have the ability to promote one BOFF to Captain once you reach RA/VA? You would still give the orders, as your the senior ranking officer. Would just be more in keeping with a military ranking structure.
I agree with you. An Admiral is not directly in charge of a ship, he is simply on the ship (in this case) to control a larger fleet action (or squadron), he is "Flying his/her flag" from the ship, but the "Flag Captain" is the person that actually runs the ship.
We should definately be allowed to promote a Commander to the rank of Captain (and call it Flag Captain if you want).
I am not too sure what abilities they could do, or how to work it out correctly, but I love the basic idea.
From a lore standpoint, I have to take the current state of the Alpha Quadrant into consideration for this one. It's been established that with the Undine infiltrating every major faction in the Alpha and Beta Quadrant and putting everyone at each other's throats, along with the Borg being increasingly aggressive, the Federation needs as many commanding officers as it can get. They have the resources to fit newly trained ensigns to take control of their own starships simply because they don't have the personnel to man all the firepower that they can provide.
Under normal circumstances, an Admiral would give up command of his ship and take on a desk job, and usually you wouldn't be allowed to promote a certain number of people to a certain rank (The reason why Harry Kim remains an Ensign throughout Voyager is because they just can't allow for any more lieutenants among the crew roster of Voyager) but with the Federation needing every person they can right now, it's best to allow captains to become Admirals and obtain better ships, while still remaining in command.
it's for this same reason that us Admirals are taking orders from lower grade officers for missions. It's THEIR job to be in command of those operations and provide us active captains with the orders to carry them out, because they know more about the situation as we do.
Now, getting to the point of promoting our BOFFS to captain: I would say that promoting them to Captain would qualify them to be in command of their own vessels. While it would be cool to see an Admiral with a fleet of ships under his wing, each being controlled by the captains who used to be his own bridge officers, this would leave everyone a little understaffed for their own ships. That's why all your BOFFS remain as Commanders.
On my KDF side My Main is a Tac Captain, his minion is the science alt. The have all the same BO (minus one or 2). The main also has a BO of the Sci Captain. Since they are both "alien males" I can swap their looks and even the alien soildier-type as a costume.
Once we can change our captain's race and gender, I plan to make my Tac alt (which is now the same as my Eng main) to be like my current First Officer. The Sci alt I might remake into my CMO, if we can ever get Deferti or more alien parts