The way I could possibly see A.I fleets working in Starsector as it is now would be to have them as automated sentry fleets that just guard valuable player owned property, like stations.
I feel it should ideally be kept simple, with more time spent by the player setting it up initially than time spent constantly going back to and maintaining it later. So, set up fleet specs, and leave. You only should have to come back to it if the fleet needs military assistance or the station's supply lines have been severed.
The settings for fleet size and configuration could all be under one U.I tab upon landing at a player owned station. To handle ships, this system could import variants (either default or custom from the player), and use resources from the station's stockpile to automatically assemble/equip and launch the defense fleet/s.
Mayyybe, if time permits and it seems reasonable from a design perspective, some kind of longer range patrol routine could even be set up to protect trade routes between systems, but the more complex the orders A.I fleets can take, the more difficult it is to get the whole thing to work without bombarding the player with complex u.i, a high learning curve and a huge amount of micromanagement time.