I don't know how feasible this would be (I'm not a code guy, or a scripting guy, or anything like that), but having capship AI that prioritizes incoming bombs would be wonderful. Really, think about the crew of a turret on the side of, say, a Deimos. A gigantic anti-matter torpedo is barrelling straight for them. What do they do? The continue plinking away at the tiny little fighter that can't even muster the firepower to really damage them. Then again, it might break game balance a little for escort missions.
It might also be cool to have a groups of turrets on the hull that co-ordinate to try and take down fighters, or prioritize one type of craft over the other, or something like that. For example, have flak turrets prioritize bombers to keep them from launching, have AAAs prioritize fighters because, realistically, they have the greatest chance of destroying them, have blobs engage either, have large beams engage either bombers (slow little things) and other capships, have Slash beams engage fighters or actually aim for subsystems. Stuff like that, or have several different kinds of turrets grouped to all fire at the same target, simulating group fire control, or something.
Right now, the capship turrets feel too much like they're all operating without bothering to talk to each other, or don't have their priorities straight.