kill it, replace it with a series of toggles. Maybe make officers inherit sets of available options for those toggles and then let the player pick new ones to unlock as said officer levels up, and have the Command HQ unlock the ability to customize presets that will spawn at your market.
Obviously this would have to be done to coincide with a rework of the AI & would have to be one of the final features added into the game since AI is a system that touches on most other mechanics, but there's so many edge-cases where one-size-fits-all that I think there's a case to be made for preset AI suites being axed.
For example; does this ship count its PD weapons as weapons or defenses? Does this ship join its fighters missiles & close support in the fray or merely deploy them? When escorting a bigger ship, does this ship merely lend it close support, take cover in its shadow or join the fight? When escorting a faster ship should this one try to keep up or automatically issue a sub-order for the target ship to escort it to stay together? Should this ship use its missiles for finishing or as close support? Should this ship manually use one of its weapongroups of non-PD guns against missiles or never? Should this ship save its ship system offensively or save it for escaping? Should this ship leave the combat zone once its out of limited use weapons and systems or not? Should this ship use its armor to press an advantage or never? Should this ship die for the cause or live to see another day? Should this ship avoid pressing the advantage on an enemy surrounded by backup or brave the danger for glory? Should this ship prefer to run down slower and weakened enemies or focus on the battle? Should this ship place the salad fork on the left napkin or right napkin? Does this ship use its HE payload to overload shields when it can or save them for after the overload? Does this ship prefer coke or pepsi? Should this ship consider its missiles fighters & close support to be its primary armament or use everything non-PD for ranging or is it primarily here to screen missiles & fighters?