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.