I think the current implementation of this is limiting different tactics in pvp. In pvp, everyone is running engineering team and other repairing abilities on constant basis, wich kinda nullifies the potential effect of disabling abilties, like phaser proc or target subsystem.
My proposal, that each subsystem takes at min. 5s before is repaired. And also that the time is dependant on current available crew. The less crew available, the longer it takes...
Thus if someone disables your shields and you use emergency power to shields/engineering team, it takes at least those 5s to get them up.
P.S. And yes, as someone who runs disabling spec atm, im very anoyed