Something along the lines of if you are +100 with a faction you can fund fleets to them, pick the ships, crew, fittings and let an NPC control it. I was thinking it would tie in with later possible additions like faction warfare, where you could beef up a faction to allow it to defend/conquer better. you could also fund the pirates with phase ships and descend the sector into anarchy if you felt like it
One other thing i thought would be a good addition that would tie in with the "Officer" tab, you could have smaller fleets that normally function within your fleet, but you can have splinter off and do your bidding. For example, if you have a Huge fleet, you cannot sneak into a station. but, what if you could split off a few frigates to go dock with the station instead? you wouldn't have to dock with a nearby station, store your fleet/cargo/crew/etc. Or, like how the Larger factions have the Fast picket fleets [ really annoying by the way good job ] that intercept you rather quickly. you could have say a wing of talons or wasps orbit farther from your fleet that you can control separately in the map, using to pursue fleeing enemies. Those Could be commanded by your officers.
Thought of this coming home today, maybe you could set your secondary fleet to intercept/strike/harass like you can do in battle?
i hope that was clear, i am better at reading than i am at writing.