After several false starts I hit the end boss with my Torus ship, and beat the snot out of it. Weaponry: Starting heavy ion 2, an auto laser, burst laser 2, heavy missile drone, heavy anti-ship beam drone, light anti-crew missile drone. Extra systems: Mind control and Cloak, subsystem Battery backup. Augments: Drone recovery arm, Engi med-bot dispersal, and Teleportation disruptor.
I also have the Captain's Edition installed, which is where some of that is from(new drones, teleport disruptor).
I found the mind control system somewhat useful to disrupt the enemy, but often it was more useful to just counter enemy mind control with it(even the first level breaks enemy mind control if you target your own guys). The hacking system is probably the better system, though mind control+boarding should be excellent, but that means you won't have cloaking, which is extremely useful for the final battle(cloak when boss sends out his mass missile salvo or bunch of drones to avoid most damage).
Backup battery was very useful in the boss fight, even with 3-4 zoltans onboard, powering everything is tricky.
Sidenote: Don't get the cloning bay if you've got Engi med-bot dispersal, the augment stops working without medibay, learned that the hard way, and didn't get the cloning bay on my winning run.
