I've been playing FTL recently again to try and beat Hard with every ship, but the Fed/Matnis/Stealth/Zoltan C ships just refuse to work out. How did you deal with them?
In playing hard mode, I've discovered that Mind Control paired with some weapon that sets fires is a very potent combination. Set a room on fire and control the first guy to rush in, and now the crew can't put out the fires while the controlled guy is around, giving it plenty of time to spread and burn down the system. My first run with the Engi C was able to capture about 70% of the ships it ran into - deploy a Hacking Drone to drain the shields, shoot a Fire Beam to cause a ruckus, and Mind Control the first sap that manages to get into the shield room.
This tactic doesn't work well on ships with a Rockman and a Level 2 Medbay, and of course Lanius and Auto-ships don't care about fires at all. Still, it carried me to the end of the game pretty smoothly.
In playing hard mode, I've discovered that Mind Control paired with some weapon that sets fires is a very potent combination. Set a room on fire and control the first guy to rush in, and now the crew can't put out the fires while the controlled guy is around, giving it plenty of time to spread and burn down the system. My first run with the Engi C was able to capture about 70% of the ships it ran into - deploy a Hacking Drone to drain the shields, shoot a Fire Beam to cause a ruckus, and Mind Control the first sap that manages to get into the shield room.

This tactic doesn't work well on ships with a Rockman and a Level 2 Medbay, and of course Lanius and Auto-ships don't care about fires at all. Still, it carried me to the end of the game pretty smoothly.