FTLs main flaw imo is it's main asset - the randomness. Sometimes you get lucky and find a ton of crewmen and great equipment on the way to the last sector, sometimes you find nothing. And no matter how skilled you are, you need that def drone mk2 to even think about surviving a barrage of missiles from the mothership.
Pete - improve the blast doors if you haven't already - they stop both the fires and boarding parties. Upgrading them also gives you manual control over them so you can for example seal off a part of the ship where the enemy is, or where the fire is raging, or both - and vent atmosphere by opening the outer door.
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