I just ran a few simulation tests for quick and dirty casual observations over several duels.
* AI rarely uses two Fast Missile Rack charges before recharging once.
* AI sometimes uses a charge to open with a double missile attack (like a super move in a fighting game).
* AI sometimes uses a charge when it wants to fire a missile now and uses system once to enable that action.
Player pilot is the only one who can consistently use more than one charge before the system recharges.
Alex removed charges from Quantum Disruptor, so it is not unprecedented that systems had charges removed for some reason.
My suggestions:
* Remove all charges from Fast Missile Racks; FMR only has cooldown, just like Quantum Disruptor.
* If FMR is ready, AI use the system immediately after firing all missiles it can during its window of attack.
* Maybe using the system costs no flux, just for ease of use.
Basically, treat updated Fast Missile Racks as a variant Accelerated Ammo Feeder that can be used similarly at the earliest opportunity by player and NPC alike.