At first, it may seem odd that the supposedly oppressed Rebels are treated as the game's villains. But not only is The Federation shown to be perfectly democratic, The Rebels themselves are human-supremacistpolitically incorrect villains. Specific emphasis is given to the issue of slavery, with rebel-employed slavers being treated as the worst of the worst. Building on that, it's made clear that these rebels are extremely powerful and that this civil war is encompassing pretty much all federation owned space. FTL is the American Civil War, IN SPACE!!!
There's also the implication that, for all the strength the Rebels had where you were, they weren't doing so well everywhere else since they were so focused on you. That's how the Federation was able to defeat the Rebels so quickly once the Flagship was defeated. This also accurately reflects the Civil War, where the South was only strong in the Eastern theater but was losing everywhere else. The war was only well and truly over once the Confederacy's 'flagship', General Lee, was defeated even though the Confederacy had been eviscerated in every other theater by that time.
It's odd that the game will refer to "your crew" even though there isn't a single perspective character. In fact, you can turn over your entire crew due to random deaths, and still continue playing, still occasionally getting event messages in that second-person perspective. But then you realize its possible to lose while you still have crew intact in a boarding party on an empty enemy ship... "you" isn't the captain, or any other member of the crew, "you" are the ship!.
Perhaps there's an in-universe explanation for pausing and giving you control of targeting, doors and power management. You're the AI and pausing is just your processing speed. It's probably way faster than humans but you still need crew to man systems probably because politics and morality, but also to repel boarders.
In some fights with Rebel ships, the enemy ship will attempt to warp away. Allowing them to do so increases the rate of pursuit from the Rebels, now that they have info on your location. However, if you warp away first, nothing happens, despite the survival of the enemy ship. Why is this? Because you could've warped anywhere! When the rebels flee, they report your last known location, but when you flee, they have no idea where you could have gone.
Why would a ship with no shields lie in wait in an asteroid thicket, and how do they survive for long enough to (foolishly) engage you?
The only ship with no shields (usually) would be Auto-Scouts. They survive long enough because of their crazy-high dodge rating (making them occasional Goddamn Bats).
That, and because their (automated) system deemed your attacks to be of higher priority, those drones stopped dodging the asteroids when you started fighting them.
Why does nobody use space suits (except during EVA)? They'd be very useful for repairing hull breaches or disabling the inside of automated ships.
On that note, why aren't there any emergency oxygen masks on any of the ships? They would definitely let crewmembers operate depressurized rooms for the duration of a single battle. You'd expect them to be as common as life vests on boats, but they don't exist until the Advanced Edition ... where all they do is halve health lost from asphyxiating. OSHA must have been the first casualty of the war.
I think that rather than being a casualty of war, it was a casualty of peace. Think about it, with the Federation existing for probably a really long time there likely weren't many situations where people had to fight. That, with the advent of shielding technology and automated repair drones, means there weren't many situations where people would need to wear those suits; oh, sure, they had to deal with pirates sometimes and all that, but even then the usual "feed it more power" solution that upgrading the oxygen generators is worked most of the time (unless their ships were falling apart, in which case they die anyway), and when the Federation was in its prime even that might not have been an issue. And the suits are uncomfortable to wear, and both those and the emergency oxygen masks take space, space that could be used to enhance the ships in some other way. So when the rebellion started, they did not have the suits ready, and the Federation did not have the resources to start using them whereas the rebels were still feeling confident and thought they don't need them (the standard "Titanic doesn't have enough boats but it's unsinkable" train of thoughts, only in space).
However, as time went on, and due to continuing negotiations/alliances with the anaerobic Lanius, the Federation needed to come up with something to stop the Lanius from accidentally killing their crew-mates with their oxygen-destroying bodies. Enter the Emergency Respirators augment. Due to most of the money going toward stopping the Rebels from absolutely crushing them, they aren't perfect (everyone takes half-damage from suffocation), but they're something.
The Cloaking Device will increase a ship's evasion rate... which also somehow extends to stray asteroids inside of asteroid thickets, as if they were projectiles aimed at you by someone else.
Many blue options can reveal things that can defuse situations peacefully, even for the better. Example? A Lanius cruiser is chasing a civilian ship. You can intervene and defend the civilians. The blue option of your lanius member reveals they're just friendly merchants looking to trade.
Assuming that your crew wouldn't do anything on their own unless you command them, what's going to happen to your crew after you destroyed the Rebel flagship and your ship is left in critical condition (say, everything is on fire or the oxygen system is disabled)?