So right now system offline skills(like target subsystem weapons or auxiliary) are pretty effective in PvE, right? but what about PvP? Well, most players have emergency power to shields or weapons or whatever their primary power is for their ship.
Knowing that, target subsystem skills or boarding party or whatever skill you can utilize that takes a system offline is almost minuscule in effectiveness in PvP.
A large problem ive already noticed in PvP balance are certain skills like reverse shield polarity, or the very much annoying feedback pulse, or the mass of buffs an escort can stack to utterly destroy you in a matter of seconds. For example if I utilize photonic officer with 2 ranks of Reverse shield polarity, i can essentially be immune to energy weapons for a minute straight, and have a 30 second gap in between the first minute and starting up a new minute. Seems a little OP.
What i suggest is to change the various skills that take a subsystem offline to not only take the system OFFLINE, but remove any buffs that system has active with the EXCEPTION of emergency powers and other skills that have the specific purpose of restoring offlined' subsystems.
If completely removing a buff seems a little extreme, at the very least reduce that buffs' effectiveness.
This is definitely a drastic change to the PvP world, but I think it is completely reasonable, and would even force players to pick and use their skills more wisely...