So Fleets get cumbersome in large empires, however I think I have a quick way to help, and I've managed to get a way to implement it without actually requiring much of a change to the interface, and in a way that would be easily handled for the AI, even though really this doesn't need to be implemented for the AI except in the context of the AI Automation for ship actions.
Simple Solution : Let us assing other Fleets as Home Bases, and thus create Sub-Fleets.
Everything else would remain the same, Stances, Automation, Ranges, Everything. But this would let those of us who play on massive maps and thus tend to have lots of fleets covering a lot of space organize our fleets better. Furthermore, it would naturally scale emergently, as you would be able to assign a Sub-Fleet to a Sub-Fleet. In which case this Sub-Sub-Fleet's Home Base would move with the Sub-Fleet.
So for instance if you had a Fleet with a Sub-Fleet Taskforce set to Defend Target and Nearby Systems that Taskforce would defend any system near the main Fleet. If that Sub-Fleet had a number of Squadrons assigned to it with the Defend System stance, then those Squadrons would defend the System that the Taskforce was operating in. Thus the Taskforce might move to a system near the main Capital Ship, and the Squadrons would follow and then automatically begin operations in this system.
Furthermore, it would make it easier to have Resupply Ships in fleets. In my games, I tend to use Resupply Ships as my Super-Capital Ships, and the Flagships of my major fleets. I would be able to make the Resupply Ship the main fleet alone, and then put all of the actual combat ships into Sub-Fleets, with some small Squadrons set to Defend Target, thus they will stay near the Resupply Ship and serve as its escort, and several Task Forces set to Attack Nearby Systems, thus I could just move the Resupply Ship to a new Staging Area and let the Sub-Fleets naturally pursue their objectives.
This builds naturally on the existing system, and really the only Interface Change I could see being necessary is auto-indenting of Sub-Fleets in the Fleet Viewer, although being able to expand and collapse the Fleet Hierarchy would be awesome.