I would settle for being able to save and load fleet configurations (using either a 'warning X missing' or best-fit substitution system) since right now dismantling and reconstituting fleets is so laborious. Why drag every ship you might need around with you when you could quickly swap your Bounty fleet for your Smuggling fleet?
I can think of a whole mess of options involving player-owned AI fleets; command-shuttling between fleets, ordering fleets to follow your fleet or follow a target fleet (also; it would be nice to have a command to match speed with a fleet to shadow it), splitting fleets, etc. that may or may not be viable for the existing game. All of that crap would be nice to have, any of it might reasonably be too much work or not fun. On an abstract level, I'd love to have AI fleets to perform some tedious tasks for me (like retrieving weapons or cargo from storage and bringing them to me, or to a nearby port where I have storage space, or guarding my base of operations), but heavy fighting is too much fun to let the AI do for me.