This vital tactical function needs tuning. I hate when my manually patrolling destroyers go on some wild chases outside of my systems. Engage system targets should ONLY mean engaging system targets and not leaving important strategic points without protection. Even worse is that they don't return back to their manually set tasks and just keep on sitting there in the middle of nowhere. I play the game on the complete manual setting and having to deal with this every single time is quite infuriating.
In my opinion, it is an enormously frustrating aspect of this game to assign a fleet or ship to a strategic position and then have it run off on some pointless mission a few minutes later. I have tried all of the "Engage Nearby, Engage System, When Attacked" commands and ships seem to follow that instruction for just the shortest time, and then run off and do something totally irrelevant anyway. A corollary to this is to have a Construction Ship with 90% fuel and when you tell it to Repair X or Construct Y it heads directly to the nearest refueling station. Repeat the command as often as you like but it will not do it without refueling first. Grrrr. [:@]
I can understand your frustrations. Although I've noticed in my games that if I
order a fleet or vessel to do something, then take it off automated, it usually
reacts to its orders according to the battle stance it has. Don't get me wrong though,
I hope that Elliot does get around to fine-tuning this element of the game. [:)]