(Text from the photo album)
For the first couple sectors I boarded with Mantis, because engi are basically useless without a strong support system.
As soon as I could, I moved all my mantis into manning positions and boarded with non-mantis -- first teleporting a human and Rock, then following up with the Engi.
This autoscout was a gift. I was able to train my Engi without fear of repercussions. They could do two damage to the system before I had to teleport them back. With L3 teleporters the whole process was pretty quick. Finally, two +20% combat Engi! Now to find two more...
I found one fully trained Engi in a store, dismissed my human boarder, now I have three Engi and one Rock.
Reconstructive teleport was very important as I was able to keep my Engi trained. I also had a fantastic weapons setup.
Eventually I found my fourth Engi boarder. He was a trained pilot though, so I killed him 15 times in a clonebay deathtrap in order to de-train him. Soldier, forget what you think you know! On this ship you kill with your hands!
Mind control was a wonderful addition. I had the option to use cloak or hack but felt they would lessen the role of my Engi boarders.
This was the hardest ship I fought. Six crew (two humans, two engi, two mantis) with mind control. I was finally able to kill them all, but it took a lot of time.
Flagship Phase 1. My teleporter got hacked, unfortunately, and it would have been impossible to keep the enemy hacking system offline, so I had to use conventional means to win.
Flagship Phase 2. Four engi plus a mind-controlled human. This took a long time, but thankfully my defense drones and high shields kept me relatively safe while I slowly whittled away at the enemy defenses.
(I hadn't realized it but a mind-controlled enemy had managed to sneak on my ship and was in the process of destroying my clonebay!)
Flagship Phase 3. There was still a lot of enemy crew left and the enemy mind-control was difficult. At one point MY mind-controlled mantis was fighting THEIR mind-controlled human!
Eventually, though, I was able to down the zoltan shield and put some pressure on. The shield did regenerate, much to my dismay, but it's a lot easier to take down the second time if you already have boarders that are disabling piloting.
Finally all the enemy crew were killed. From there it was mostly a matter of time.
Here are the skill levels of all my crew. As you can see, all my Mantis and 3 of 4 of my Engi were fully trained in their skill of choice. I do have a +20 combat mantis and a +10 combat mantis from my early-game boarding, admittedly. Eh, what can you do.
It was an extremely fun run and I learned a few new tricks with mind control. I also learned that L3 teleport is AWESOME for 2-man teleporters.