This may seem to be the case, but as the scale of play approaches my desired heights(small SINS scale, dozen planets+,200+ ships) it's simply the level of abstraction necessary to enable workable play. One of the things I always disliked about the C&C series was the units were not capable of acting on their own in any reasonable fashion...you could drive an army into an enemy base and they would just sit there after clearing the offensive units...ugh. Compare this to Total Annihilation - where you can ignore entire non critical battlefields after issuing your overarching commands. Setting simple behavior tags such as "Fire at will/Hold Fire/Return Fire" and "Hold Position/Maneuver/Roam" create surprisingly complex results.
That said, and to the question of the user being a mere spectator, Any user commands (to include setting target, where to move) override the behaviors system until that command is completed. If the user tell a ship to target a particular enemy, they will do so until they or their target is destroyed...same for movement. For super heavy weapons this is critical.... you shouldn't waste nukes/blackholes/asteroids /mirv weapons on small fry(the cycle-time/cooldown is too long) .
As for the AI changing targets mid way, a weakened/crippled ship's attack value is higher then a fresh one...they make a tasty target! Ships that would not normally risk engaging them may take the opportunity it get some shots in.
There is no friendly fire at this time because it's simpler to handle the collisions...If I have to start checking the fire lines of each weapon all the time that's allot of checks- On pc not an issue....on a single core android tablet...
That's said the decision AI does not run 1 to 1 with the stepping, in fact its semi random within a given range but typically it takes several seconds between a single ship target preference check. When there is not a preference or the preference has been destroyed or lost contact with they revert to targets of opportunity.
Those tracking missiles actually are targeting on individual parts of a ship, so if the part is separated from their parent the missile will continue to track it. If the part completely vanished before the missile impacts they go dumb until they time out, there is no redesignation. I like things to be able to miss!
Mines exist currently but do not actually have a AI deployment method....still working on that one. I hadn't considered chaff/decoy's which is an oversight on my part, I'll add those ASAP. There is a EMP missile that has the ability to interrupt a ships offensive/defensive targeting ability BTW (and another that cripples engines)... Also on the weirder end of the defensive spectrum there is a "return to sender" beam that reprograms enemy missiles and fighter drones sending them back where they came from...thinking of doing a special shield with similar reflection properties that acts on a pulsing behavior(I mean, if it was always effective they'd be invincible.)
EDIT - Chaff launcher in! Clouds break track lock of enemy missiles and some direction change, making then likely to miss. Good call on that one!