@jdh5153: With the specific problems you're talking about, the doors/airlock really are the solution.
For fires, pause immediately. Open the outer doors of your ship, and open a pathway of doors to the fire, so that all of the air drains out in the room with the fire, then unpause. The fires can't burn without oxygen. Naturally, move any crewmembers elsewhere that may be in this pathway of oxygenless rooms. When the fire is out, you can safely close all the doors.
For boarders, pause immediately. Open the outer doors of your ship, and open most of the doors of your ship, except for the cockpit and medbay. If you do this fast enough, the boarders usually won't have time to destroy any one room and will instead be forced to head to your medbay or else die of lack of oxygen. You can leave your pilot in place (otherwise you wouldn't be able to dodge anything), but order everyone else to the medbay. You can now unpause. Most of the boarders will be corralled into the medbay, where you will easily win because you're gaining health as you fight. Sometimes the boarders will be dicks and send 2 guys into your cockpit, in which case there usually isn't any way of getting them out; continue fighting in the cockpit with as many crewmembers as you can fit, and whenever a guy gets down to say 33% health, he should swap places with somebody in the medbay who has more health. When doing this swap, you should absolutely pause, that way you don't accidentally take too long to save the guy with low health.
The airlocks feel a little cheap at first, but airlocks/doors are one of the main things you can do that the AI doesn't do, and you pretty much have to take advantage of that, because you're right, as early as sector 2, enemy ships (or random encounters where 4 assholes teleport onto your ship out of nowhere) will have boarding parties that are more combat capable than whatever crew you're likely to have at that point.
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