I definitely recommend disposing of the cross-system targeting, making it so only targets in the same system as the ship itself could get and/or stay assigned (as opposed to JP transits clearing them). My reasoning: I've been annoyed before by ships trying to fire at STO's that they defeated in the last engagement months ago and light years away, and JP transit target removal would help with that. But I also remember screwing up a couple of times by using the "Assign All" button in missile combat and having ships of the same class all across my empire fire their ordnance into the abyss. I don't recall the specifics, this might've happened when I was using waypoint-fired missiles, but there's still no practical reason why "Assign All" should copy targets to every single vessel in the class, no matter where it is. Not to mention that it could be used to bypass the JP target removal, were it introduced, and still make the pre-targeting exploit possible.
As for the same-increment fire, I was going to suggest removing it as well, as a JP assault is a terribly dangerous gamble and NPRs' ability to fire instantly exacerbates it further. Since max squad jump distance is randomized, getting a bad roll is the difference between sustaining some light shield damage or getting half your fleet annihilated with nothing you could do about it - not even a chance to make some distance within those 5 seconds (during which the NPR would likely try to run away too, as it often does when faced with superior tonnage, without considering complications such as jump shock - perhaps it should factor such things in).
However, the proposed change to "Fire at Will" by making it automatically acquire targets (definitely no need for a separate command) actually sounds great to me for another reason - it would greatly assist in those mop-up phases of a beam fight when the enemy is on the run and the main challenge lies in the tedium of assigning new targets as old ones get destroyed all while keeping them in your FC range. I would absolutely love an auto-targeting Fire at Will command for such occasions, even if it means it's also available for both the player and the AI for jump-point defense! Just need to make sure it doesn't cause interrupts and can't be actually used for jump-point
offense, as there's currently some very weird interactions with Fire at Will and jump shock
And if you were inclined to make jump assaults less of a gamble, why not allow us to set the minimum jump distance through the corresponding text field in the Naval window? It would sure make JP-adjacent combat feel a lot more consistent!