I'd really like to see the flag bridge integrated into the subfleet system.
So you'd have your fleet and it has an admiral who requires a flag bridge, like you do now. The required rank of that admiral must be higher than their subordinates, but also depends on the number of items (ships, or subfleets) within his fleet. Say more than 4 items and he needs to be 2 levels greater, more than 8 then 3, etc.
So in significant fleets, you'd need to group your ships up into subfleets in order to get the rank requirement to be sensible for the commanding admiral. But the system should then continue down into the subfleets. Each of these need a subordinate admiral who fulfills the same rules regarding their own subordinates, so you may need to group their ships into another level of subfleets, which again would each require their own subordinate admiral.
So you'd get a situation say where a fleet was commanded by a full admiral, and under him he has say his battleship division, cruiser division etc, each commanded by vice admirals. Then the battleship division is divided into BatRon 1, BatRon 2, etc. each containing 4 ships and commanded by a rear admiral.
I think this would feel more realistic - it would provide some jobs for all those admirals, and it would create an interesting problem of what ships to put flag bridges on to get the command structure working.
To avoid annoying people you'd need a way of opting out. Say if a subfleet doesn't have an admiral then it just doesn't count at all towards its parent's requirements. But it and its subordinates do not get any commander bonuses at all.