Strongly disagree.

1.) Subsystem targeting requires a very high Flow Capacitors score in order to have a meaningful impact on the target. So there's an added level of infrastructure cost.

2.) The ships most likely to use beam arrays don't have the tactical slots available to use subtargeting abilities.

3.) Subtargeting has a 45 second cooldown with 10 second active time. Power-efficient dual cannons do more damage all the time.

4.) Subtargeting does not increase your basic damage output. It can create a vulnerability on the target, but without damage output to capitalize on that vulnerability it's a useless ability.