My problem is simple.  your own ships have an AI of their own, meaning they will actively seek out targets if left alone.  however, I have a problem with that.  say I want to bombard a planet or destroy some structures.  well everytime someone jump drives into the gravity well, they always quit what they are doing and go right for that ship, even if it is just one scout, or ships that are turning around to jump drive back out as soon as they jump in.  I've tried changing engagement range with no luck.  it actually seems as if engagement range does nothing at all, since even if it is set to local or anything at all, they still stop what they are doing to chase after ships anywhere in the gravity well unnecessarily. I would think an extra option would be useful, such as engaging only ships that have shown to be hostile (firing at all on you or your structures), or to have only scout ships attack other scout ships because scouts will usually outrun most other ships in most cases, making any chase useless. 

another problem I am having is fleet cohesion.  no matter what it is set to, in a large battle on enemy worlds, they are almost always compacted and surrounded if you don't tell them to move here or there constantly, basically making them into a giant ball of crowded ships that are reminiscent of shooting fish in a barrel.  the whole point of a loose cohesion is to be spread out so that it makes it harder for weapons fire to hit multiple targets easily.  maybe an option like setting ship to ship distance specifically could help, especially if they maintain that as much as possible.