What if you literally make the Huske System? You could make the various player fleets flying around near a central point (for ease of access to each other - more on that later). The "Observer" fleet (the fleet that you're moving around on the map) would play no part in actually doing any of the fighting, only to tour the system and manipulate what fleets attack each other (more on that later as well).
OK, to the Player Fleet AI. These fleets will be neutral to each other at all times, aside from when they decide to pound each other into the stardust on the command of their admirals. Now, I'm not sure if you can set these fleet to be the same faction, yet able to attack each other on command of the Observer fleet. If they can, the easier it is to implement, otherwise you'd need a separate faction for each fleet. Also, these fleets can be easily edited to add or subtract ships and edit variants through the save file.
OK, to the actual Player fleet fighting. It's be as easy as clicking three buttons, first going to a station to bring up a dialogue. Next you will choose the first Player fleet, then the next, similar to the beginning of a new game in vanilla Starsector. These who fleets will then be ordered to attack each other (but not become hostile to each other, to save these two fleets from killing each other while the Observer isn't watching). They attack, break off, and the battle is documented in the Text that comes up in the bottom-left of the screen.
Alright, this sounds like a god-awful amount of work (to start off with). But, if I can see the future correctly, it'll make the battles much easier to do. The way that players input data could hopefully be done in the same way as it has been before.