Yup - shields and your own guns... Higher rated/higher class powerplant/distributers would also be harder to take down.
They are merely another weapon, they don't damage your hull, however. They take shields down as normal, then instead of damaging hull, they take down a "system" as though it were a hull. At 0%, the ships powerplant is overloaded/distributer fuses popped/whatever, and a reset period of, say, 3-5 minutes is needed for it to kick back in.
Yes, there is the possibility of ganking in some ways, but really, that's already possible.
It also means there is potential for kidnapping missions, for example.
"Hi CMDR, we got word that the head of Impederiance War and Finance department (Presidents wife) is being flown to system Comegetsome in a Python. We need someone with the skill to knock it's systems out so we can board and take them prisoner, this could turn the tide of the war - you are th eonly one we know capable of such a mission!" blah blah...
Z...