Awesome! This is the type of thing that the base game needs (I was going to get around to posting in the suggestions forum eventually...); Alex said he didn't want the player to [have to] micro his AI-controlled ships and that's why it's the way it is now, but there aren't any sort of general fleet commands like "stick together" or "retreat when heavily damaged" etc so I still end up needing to micro my dumb AI companions anyway.
As for mod feature suggestions, I'd say work on things the command UI doesn't do very well right now (so make "cap points" a low priority for example). A "try to flank" command might be useful, the AI kind of just mashes together in the middle with a few random ships flying off into the distance right now, and doesn't do any flanking except incidentally. Also, maybe a hullmod to stop PD weapons from firing on ships larger than frigate class, it's kind of annoying when my PD weapons waste their charges on a destroyer and then I get pelted with missiles that they can no longer effectively shoot down.