Assuming you start at 100% oxygen repairing the system usually isn't too much of a priority. Most battles will finish long before your oxygen drops to a dangerous level.
Nonstop attacks from enemies with missiles DOES make it impossible, especially if, as I'd said, shops aren't selling good stuff. Or intended to say. I think I forgot what I was saying halfway through it and ended it prematurely. If you start off with a defence drone, it makes it much easier to survive missile ships.
You keep asserting this, but in hard mode most ships have missiles and it's still perfectly beatable. "The shops aren't selling good stuff" just isn't really possible - you will almost certainly find one of those things in the course of your game (assuming you didn't start with them).
Shields were at level four, evasion was about 25%, which in hindsight, I should have made higher. Thing is, shields were mostly negated by their hacking drone. It lasts long enough to completely drain your shields, and then the lasers fired right when they started recharging.
If your sole defenses were level 4 shields and 25% evasion then it's not at all surprising you lost. Shield hacking is a pain, but you can generally jump away if that happens (assuming you didn't massively neglect your engines).
I lacked any other systems because the game fucked me over in regards to shops. Very few systems, shitty weapons...
charge laser MK II, flak MK II, heavy laser MK I and a dual laser.
You're seriously calling this a shitty weapon loadout? Flak II is enough to take down shields on its own, then your lasers would be able to absolutely go to town on their systems, crippling them and dealing massive damage.
Those weapons are way better than what I normally beat the flagship with. If you had non-awful evasion/could retreat after the shield hack you probably would have won. So in other words the thing that fucked you over was the fact that you didn't upgrade your engines, it was nothing to do with the RNG (unless you were expecting to evade in spite of your tiny chance to do so).
For the boss, I find this is true for systems:
Cloaking: Near-vital due to the drones and the laser bursts
Hacking: Useful, but not vital
Boarding: INCREDIBLY useful. Again, not vital, but it makes the fight a LOT easier.
Mind control: Pretty useless
Drone control: Can be useful, can be useless.
Backup battery: I almost never use it, so I find it near-useless.
Cloaking is pretty great but 45% evasion + 4 shields is usually sufficient, particularly with hacking to prevent their missiles from going off. Mind control has some fair uses - you can reduce their evasion by hitting the pilot, you can abduct people from their ship in the first stage to kill them and negate their mind control in the last stage. Drones are great providing you have a good drone (if you don't then why did you buy drone control?). The backup battery is cheaper than the extra reactor power, I guess, so it can be an ok bonus.
The 2-3.
Well uh... I guess that's sortof true. Although then again those three strategies are so general that they cover basically everything you can do in the game.
Yeah, I actually beat the first two stages and then everyone suffocated because they hit my oxygen again. Seriously, WTH?
And yeah, I did do the door opening with hull breaches. Though the second time I didn't KNOW I had breaches, in my defense.
You suffocated because you vented your own ship of oxygen, not because they hit your system. You should know you have breaches due to the sound effect, but if you miss it then you should carefully watch your oxygen percentage after opening all your doors. If it starts going down rapidly you have a hull breach and you should close them until you've identified it.