The Drone phase is the hardest boss phase. I found the 3rd phase to be a fair bit easier. My tactic was to use a crack boarding squad to take out important rooms and generally reduce the crew members. One thing that helped me was that the weapon systems are separate to the rest of the ship, so if you can take out the crew there and damage the system, no one can repair it. Bombs were my weapon of choice against the boss, but you require a massive store of missiles to make it work. I should note that I had maxed out cloaking and the fire while cloaked upgrade. Careful use of the cloak really reduced the damage I took.
Stealth ships are annoying, especially if they have the upgrade so they can fire while cloaked. The best way I've found to beat them is to have cloaking yourself.
