I added Drone Control and Mind Control to the Cloak and went on to victory in the Easy Kestrel B game, as well as winning 2 more Easy games on the Fed A and Engi A, unlocking the next models of each. With Easy, I had a fair amount of scrap, but still needed some luck to put together good combinations of Weapons, Drones, and Augments.
Mind Control does work well both for boarding and counter boarding but in my experience (which may not be complete) it's weak apart from that. Keep crew separated with 1 crew alone in either Sensors (definitely a waste for the Flagship battles) or Doors and the AI targets them. A few times they controlled 1 of 2 Zoltans in Shields but they never caused serious harm. Leave them alone and they'll get better. Or use your own Mind Control to counter if you have it and it's idle.
Hacking was used against me and I found it more frustrating. Hitting your Weapons or Shields is the big threat. I've been lucky so far, apart from a battle in the Fed A game (right after my very first jump and got hacked in one of them, can't remember which, and would have died without the Artillery Beam). Need to be able to counter Hacking better.
But I found I had more to relearn about efficient scrap management, not buying the wrong item (like a Chain Burst Laser at all, or maybe not a Weapon Pre-Igniter when you already have a full battery of fast weapons like a Burst Laser II and 2 Ion Blast II's), better fire control, and better counter-boarding (lost at least 2 crew to stupid mistakes).
In more detail... (too bad [spoiler] tags don't work >:()
All 3 games at the end I had maxed Reactor, 3 Shields (Fed A could put up 4 but never had the power free), and maxed 8 levels for Weapons.
WIth my Kerstel B on Easy with the Cloak, I decided to buy Drone Control and Mind Control at that store. Rest I can't remember if they were purchases or fortunate finds. For crew, besides 3 Humans, I had 2 Zoltan for Shield Control (always have 1 Shield despite Ion attacks) and 2 Mantis for strong counter-boarding. Had Weapons Heavy Ion, Flak I, Burst Laser I, and Breach Bomb II, along with a Defense I and Boarding Drones. Augments were Automated Re-loader and Engi Med-bot Dispersal.
1st stage of the Boss battle was a bit rough for me. Doors got hacked but focus fire took out the Flagship's Hacking. Even my level 3 Mind Control (on the Triple Missile gunner mostly) was really just an irritant back, with enemy return fire taking out its level 3 and setting fire to the adjacent Oxygen System, but vacuum venting and the 2 Mantis and 1 Human damage control party dealt with that. My Boarding Drone went straight--into the Beam Weapon bay.

And I forgot to depower him after he killed the gunner and destroyed the weapon. Due to focusing on Hacking and the Cloak (why?!?) I didn't take out the Triple Missile Launcher nor kill any of the rest of the crew, despite using 11 Breach Bomb II's on top of the ion and laser fire. My Hull was down to 17 when I finished the stage and then 14 after a avoidable fight with another Rebel ship.
2nd stage went much better. Hull down to 10 but better fire direction took out the Flagship Triple Missile, Engine, Medbay, and Shields. 2 Mantis on counter-boarding and Ion focus fire on Drone Control dealt with enemy Boarding Drones. Appropriate Cloaking dealt with the Drone surges. Flagship only had 2 crew left when it jumped out, 1 in the Triple Pulse Laser and another fixing their Shields. This time I waited for the Flagship to come back.
3rd stage I started with using my Mind Control to counter the Flagship's. Last main hull crew teleported into my Drone Control but the 2 Mantis quickly finished him off. Focus fire on the Shields and the Triple Missile and when the Zoltan Shield dropped a Boarding Drone in the main hull crippled it. After its Mind Control was gone mine kept the Triple Pulse Laser crew busy until it blew up. (Getting to Sector 8 unlocked the Kerstel C.)
After that, I had another 2 games, both on Easy, with the Fed A and the Engi A. Worst battle I had was the one right after the first jump with the Fed A in Sector 1. Got hacked in either my Weapons or Shields, can't remember which, and I almost died before the Artillery Beam finished him off. Because I was going for the Achievement "Living Off the Land", I didn't buy anything from stores other than repairs, but everything else was maxed out. I'd acquired a full 8 crew: 1 Human, 1 Rockman, 1 Engi, 2 Mantis, 2 Zoltan, and 1 Crystal (never got the 3rd step of the Crystal Cruiser unlock arc, damn!), as well as Fire Suppression.
Besides the initial Burst Laser II, I'd also picked up 2 Ion Blast II's and an Automated Re-loader. With 3 gold-rated gunners (one Mantis, the Rockman, and the Crystal). And a maxed Artillery Beam.

After each stage, my hull was down to 20, 15, and 10, but I played this much better. (And finished off the Ship Achievements by getting #2 and #3 and unlocking the Fed B.)
With the Engi A, I added Cloak and Mind Control, so it was the same Systems as in the Kestrel B. Crew was 2 Human, 2 Engi, 1 Mantis, and 1 Zoltan, with the last Human being a escaped prisoner from a Rebel ship near the end of Sector 7. For the Flagship battles, it had Engines one short of maxed, level 3 Mind Control, weapons Vulcan, Ion Blast II, Heavy Laser I, and Drones 2x Combat I, as well as a Anti-Drone and a System Repair Drone which were used in stages 2 and 3 respectively. Battery was maxed and finally not forgotten, as well as Augments Automated Re-loader, Battery Charger, and Engi Med-bot Dispersal.
1st stage the Flagship hacked my Mind Control, but my 6 crew were separated into the 4 Main Systems and 2 Subsystems manable. AI kept controlling the Engi in Sensors or the Mantis in Door Control, who spent the time damaging their maxed Subsystems and then fixing it back (not even a full level). With the weapons battery assisted by 2 Combat I Drones and an Automated Re-loader, plus the Cloak, didn't take any Hull damage.
2nd stage kept Mind Controlling whoever was in the Flagships Medbay, so they took it out with Missiles and Fire, as well as half-breaking my 2-level Piloting. But with the Anti-Drone added to what I used in the 1st stage, knocked it out with Hull only down to 26. Used the Battery to power the top 2 levels of Engines as well as the Medbay and Mind Control (with some power transfer during its cooldown).
3rd stage swapped the Anti-Drone out and the System Repair Drone in. Used the Battery to run the top 4 levels of Engines. Had 5 main hull crew teleport in. As the Flagship's Mind Control was ineffectively hitting a Engi in Door Control, I used my Mind Control to support the counter-boarding party (Mantis and the 2nd Human). Was helped by enemy boarders going after my Cloak, as well as some popping into the nearby airlock, who didn't do so well with vacuum and then breaking into the next room which their own missiles had set on fire.

Most damage they did was to the poor Repair Drone as it passed them by. And they still didn't kill it.

Focus fire on their Shields and Piloting with Ion on Mind Control left their Triple Missile firing (Combat Drones just didn't hit it) and my Hull being knocked down to 20 but I burned them out. (And unlocked all 3 Engi Ship Achievements and the Engi B. Still doen't know how my single Ion Blast II ionned 4 systems in the 1st Stage. Sure, I hit Shields while aimed at the Triple Missle, and then switched to Hacking. But how did I also ion Cloaking ?!? Maybe a bug?)
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