Fun game -- hadn't heard about this until it was already available on Steam, which tells me I've put in 39 hours so far. Quite enjoyable, if a bit heavy on the randomness -- e.g. being offered a weapon pre-igniter can be quite the lucky event.
Some possible interface tweaks have come to mind that might reduce tedium or irritation without changing balance very much:
1) "Choose response / course of action" hotkeys should be letters, not numbers, to prevent people accidentally choosing an option because they were busy using the very same hotkeys to retarget weapons when they pop up (particularly the "OK, you win; spare our lives and we'll give you <blah>" dialogue, which pops up during battle). The game doesn't require that many hotkeys (just weapons right now... cloak and jump would probably be the most obvious missing ones), so picking a non-overlapping set would be better.
2) If the player's ship is entirely out of danger (i.e. no hostile ship or boarders, any boarding party is back on player's ship, no asteroids or risk of solar flares, no fires burning on the ship, all breaches have been repaired, airlocks are closed, oxygen is powered and all oxygen levels are non-threatening -- basically, safe and either stable or improving) -- there is no particular reason to not have O2 back to 100% and shield points restored up to their current capacity, since there would be neither skill or action required nor drawback to waiting except tedium. I would /not/ do the same for repairing systems unless all crew members have already maximized repair skill, because there's actually some decision to be made there with trade-offs and a crewman who happens to be the one trying to repair the system when a battle ended isn't necessarily the one you would choose to get the rest of the repair XP -- the latter might be in medbay, repairing a different system, or just coming back from the enemy ship, for instance.
3) We already have pretty fine manual control over most weapon firing (exception being the artillery beam; as far as I can tell, you can either let it charge and fire when it's ready, or you can clear its charge and not have it recharge at all -- doesn't seem to offer a charge-but-hold-fire option), so it might be a useful but not too unbalancing convenience to be able to group 2-4 non-arty-beam weapons and mark them as 'fire when all weapons in set are ready'.