I've probably mentioned it before, but I think it would help a player a lot if he could control the general behavior of his units without having to manually issue orders to each one. Instead, a player should be able to issue a blanket 'standing order' to certain ships, controlling their general behavior and targeting priorities.
Generally, ships in Sins tend to pick pretty good targets, but there are exceptions. There are also times when you don't necessarily want a ship to attack enemies that it's best at attacking (it's pretty useless if your squadron of 20 LRFs go haring off after a pair of light frigates, completely ignoring the rest of the enemy fleet).
One specific example that comes to mind is that disabler cruisers, especially the Hoshiko and the Domina Subjugator, tend to pick poor targets for disabling. I find that they tend to go after cruiser carriers and support cruisers as disable targets. I'm guessing this is probably because disabler cruisers conventional weapon, weak though it is, does anti-heavy damage, which makes it technically effective against other carrier cruisers and support cruisers. What I'd like to be able to do is select a group of my disablers, and issue a standing order to the effect of 'Use disable abilities against heavy cruisers'. This will allow me to get the most out of them without trying to order 2 dozen disablers to individually disable two dozen different heavy cruisers.
There are similar issues with interceptors. Interceptors will mindlessly hunt bombers. Sometimes this is appropriate, sometimes it isn't. After most of the bombers are destroyed, I don't want my interceptors chasing stragglers while enemy interceptors chew my pilots to pieces. Other times there aren't a lot of bombers and I'd prefer my interceptors to simply ignore enemy bombers and go straight for their interceptors.
This would go a *long way* towards reducing micro management, and the game would no longer be about who can click the fastest but who is, in fact, the better strategist and tactician.