Episode 6:
First battle, you could probably have just ioned down his shield, defense droned (most of) his missiles, and allowed the rocks to tear him apart. I have dodgy luck with that though. The rocks seem to stop coming as soon as their shields are down
Ion Bomb is nice, but I loves me the Ion Blast 2. I'd have dropped the Hermes to pick up that heavy laser, and not get the bomb. But I'm very anti-missile. You've got 30, but now your entire strategy is based on missiles. And teleporting, of course
When you said "Change the position of the fighters" I said "YES!" But you lost the ion on their medbay. You should have ioned it again. The trouble with your setup is you can't finish a fight quickly, which i what you really need in a sun battle.
I always forget my cloaking device too. I forgot you had one as well!
BURST LASER 2 BURST LASER 2 BURST LASER 2 YESSSSSS. But yeah, you should already have 6 weapon power by now.
Episode 7:
It's too long to watch right now but I'll get to it. I'm really enjoying your episodes but I just don't have the time to spare.
Pending boss battle:
You've got a job on your hands there. I'd rock Ion blast, ion bomb, burst 2. Skip the repair stations unless you take a lot of damage. Try to find the shop. Sell the extra stuff (including the medi-bots if you need the money, but keep the other 2 augments) and hire anybody you can that's not an Engi. Your goal here is to have 2 guys who can teleport into that missile bay. Ideally you want 2 mantis, but a mantis and a rock is fine, or even a mantis or rock and your human. Hell, you're hurting. Pick up a human if you have to and use your pilot, moving your weapons Engi into the pilot chair. Don't send Engi or Zoltans into the missile bay, one of them will die
Use your teleporter (if you can get the crew for it) to take out missiles, then the ion blaster, then the beam. Don't worry too much about shooting until you've got those down. You won't have the manpower to take out the main crew which will make the 2nd and 3rd phases hard but what can you do? Once their missiles are down you can take down the defense drone and cloak. Once the ion is down (and your shields are not ioned) you can take those down to 3. Once the beam's down you can take your engine down to 0 if you need to to power weapons.
Then and only then start firing. Ion blast their shields and ion bomb their cloak. Shoot the crap out of their pilot and engine so they can't dodge, and then try to concentrate on shooting their doors and cloak. You want as many guys in those rooms repairing when the boss blows up so they'll die, making subsequent phases easier.
How phase 2 goes depends greatly on how phase 1 went, so I'll save discussion of that
EDIT:
Oh! If you don't get teleporting crew it's harder but all is not lost. Ignore the missiles. Cloak through the first one but just take the second barrage on the chin. Make sure you've got all 3 weapons up and essentially do what I said above about shooting. Your goal with no teleporter is just to kill that thing fast, hopefully taking crew out with the left side. You may want to keep the hull beam if you can't get crew. It'll do more raw damage but you can't concentrate fire on a single system. If you do, try to hit as many of those empty rooms in the middle right of the ship. Don't go for systems, just damage the hull as much and as quickly as you can to kill them fast. That'll also be your strategy in the subsequent rounds.
) and on the Rock B fire bomb. I use missiles only when i really can´t get anything else