Maaaan, had a cracking shot at this last night with the Engi ship. Upgraded the most I've ever done, survived well and got to the boss with almost full hull, two heavy lasers, ion cannon and two drones (defense and anti-ship). Had pilot systems maxed, 3 shield layers, all systems manned.
Just couldn't get through their shields. Managed to get a couple of shots on ONE of the missile weapons, which was soon repaired before I could get anything through. Meanwhile, they PUMMELED me with rockets, taking out weapons, shields, engines, oxygen all just as quickly as I could repair them. Didn't stand a chance!