Integrate the Naval Admin Command and Fleet Commander systems.
I feel that the fleet commander system is a bit underdeveloped, and at the same time we now have a great system of naval admin commands with automatic assignments and the promotion on demand system.
Why not merge the two into a unified Naval Command system? Any fleet or subfleet that has at least one ship containing flag quarters, becomes a naval command and can have a commander assigned, manually or automatically, in the same way that naval admin commands work at present. That commander provides bonuses in the same way that a naval admin command does. If a commander is assigned, they pick from the available flag ships and are physically present on one of them. If the fleet or subfleet no longer has a ship with flag quarters subordinate to it, the naval command is dissolved, with any subordinate commands reparenting to the next level up.
As well as bringing the automated assignment system to fleet commanders, this would give the possibility of a hierarchical fleet command using subfleets for those that want it (squadron commanders under division commanders under the fleet admiral). But in a way that only provides the same bonuses you can get at the moment out of nested admin commands, so people who don't want to bother with that aren't penalised.