Targeting priorities - my biggest gripe
One thing that has been driving me nuts recently is targeting priorities - ie which target ships choose to attack. Basically, the problem is that trade ships rank above structures. But if you are attacking a planet with a developed economy, especially one on a trade lane, trade and refinery ships are constantly jumping in and out. Your ships, especially strike craft, go after these irrelevant trade ships instead of structures.
I frequently have sent ships into a grav well, seen that there are no attack issues and gone off to check something else. I come back expecting that they've destroyed most of the civ structures. In fact they've done sod all because they spent all their time going after the trade ships.
Please make structures a higher priority than civilian ships - this is driving me nuts.