Minor quibbles:

Some of the auto-use ability AI could probably use changes. What comes to mind:

Ion Bolt - used against everything nearby to little effect - it should stick to dangerous targets. It just costs too much to be used against a Crystal Extractor.
Shield Refresh - It's used on any ship with the tiniest amount of shield damage; it should instead be used on ships that have massive shield damage.

It would be nice to have a toggle that lets you turn off fighter selection. By that I mean if you drag a box around a group of ships, it won't select the fighters as well. Right now if I - say - want to order a group of ships to do a grouped jump, I grab the group then have to order the fighters to dock. Then I have to reselect the group to get the phase jump order after waiting on the fighters.

Maybe it's just me but it seems like the Kol Battleship is small compared to the other useable TEC capital ships. It looks sorta silly when its with a Dunov Cruiser, for example.

Finally, a suggestion that occured to me in the writing of this post. If you could queue ships before you could afford them, that would be helpful in reducing empire management time.