I was thinking about something like this a little while ago. I think it would be nice to add in a short of "advanced tactics menu" that would allow you to tweak the AI for each ship/group of ships. I got the idea from Star Trek: Dominion Wars. Basically you command a small squad of starships and play through the campaign set during the Dominion War. The game was buggy as hell, but you could tell your ships to maintain maximum range or do fast hit-and-run attacks. Alpha strike, or fire weapons as they're ready. Turn off power to one system and divert it to another. Try to target certain subsystems on enemy vessels.
Naturally, all of these particulars don't appy to Sins, but it was a very nice concept that added a lot to the game. I'd like it if I could have some kind of "priority list" for casting abilities and even for attack orders. Something that would let me tell my subverters to only use their shield-damaging ability on capital ships, and only use distortion field on heavy cruisers, for example. Or maybe use distortion field on heavy cruisers first, support cruisers second, and LRF third.
Being able to tell subjugators to concentrate on healing your own ships first, and using suppression second (and even then, on enemy support cruisers first and HC second) would be really awesome.
This would probably require *a lot* of coding to add, and a lot of thought to impliment properly. One way to make it a bit easier to manage would be to allow the player to right-click on a ship type at the shipyard and get a shortcut menu. One of the options, of course, would be to cancel production. The other could be something like "give command priorities..." which would bring up the box allowing you to specify a default set of priorities to everything built at that shipyard.
Or maybe there should be some kind of empire-wide method for giving command priorities.
It really is a good idea, but I can also see that it would be difficult to impliment it well.