So I bought it a while ago but gave it a go just now.
And wow. I absolutely love this game but I just can't win. Playing on easy, I did about 6 or 7 playthroughs and I can't win with that damn Engi cruiser (tried all three layouts). So I can't unlock any new ships.
The journey up until the Flagship is a cakewalk, I think I wouldn't have any trouble on Normal by now, but I usually die in the second round of the final fight. Only once I got to the third one and died very quickly.
I even watched a few Flagship guides on Youtube and I think I did everything right (I had a pair of teleporting Mantises, destroyed the rockets first, then murdered all the crew) but the second round the stupid breaching bot starts to invade me every few seconds, plus the drones, plus the weapons, it's madness.
I wonder, what is your ratio of win-losses? Is it normal to win like 1 in 10 tries? Normally I wouldn't mind but I really want to unlock some new ship types and I don't wanna play the damn Engi cruiser over and over again. Sigh.
EDIT: Also, I'm playing with the Advanced Mode on, should I turn it off for now? Is it gonna make the final fight easier?
6 or 7? It took me 53 playthroughs to finally beat the flagship!
After several hundred games, my win-loss ratio is about 1-3 or 4, but when I started out it was... well... 1-52. It gets easier. My second win took maybe 10 more games.
I would say a win in your first 10 games would be incredible. **Some minor boss spoilers below**
Teleporting to destroy the rockets on the flagship is a very good move, but you shouldn't kill the entire
crew. If you do, the ship's AI will take over and start auto-repairing systems rather quickly. You should try to leave at least one crew alive.
It may be a good idea to upgrade your doors, and maybe have someone manning the door system, so the boarding drone will have a tougher time tearing through your ship during the second round. I would suggest not destroying the boarding drone, because the flagship will just launch more, and it will create a lot of breaches.
Finally... Advanced Mode can make the boss easier or harder. It depends on what systems and equipment you have. But I think everyone would agree that the boss fights are less complicated in standard mode, so that might not be a bad option for beginners. **End minor boss spoilers**
Also, there are other ways to unlock ships. If you have the right systems or crew during certain quests, or if you choose the correct dialogue options, you can unlock new ships. This wiki page
will tell you how you can unlock every ship.