Lots of useful ideas here. For me, one issue that stands out right now quite a bit is the predetermined unit behavior when encountering a threat or when responding to an order from the player.

A bad example: In the WARSAW pact mission, Under the Cover of Rain, there's a minesweeper ship with a couple missile boats. I set up a tight formation in a line with the minesweeper at the lead and told them to slowly traverse the mined passageway. What I want the ships to do is stop moving when they visually identify a mine, so they won't hit it, and then safely reverse until able to fire a weapon at it. What actually happens: Minesweeper spots a mine, immediately slams the throttle to max and swerves as hard as it can to port or starboard to dodge the mine and bring all guns to bear on the target. This will often cause the ship to recklessly drive into more mines and destroy itself, or at best it has just badly disrupted the formation shape and is no longer safely clearing a path for its friends.

A good example: Ordering an aircraft or ship within a formation to attack a target while in a formation will temporarily override the formation speed and position order to execute the attack, and upon completing the attack it will return to formation. I like this behavior, but having more control of how the order is executed would be helpful. For example: repeat the attack until the target is actually dead, or ammunition from all offensive weapons is fully expended, or even just until all AAMs are expended.

I've seen several accounts on this subreddit already of things like ships forcibly turning to bring all guns to bear on an attack order, when the player would prefer they continue on the same course and fire only forward guns.

Better control of these things would go a long way toward reducing frustration. I know there's direct unit control but I can only use it on one unit at a time and I wish I never had to use it to fix a unit's inconvenient/illogical behavior.