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 it's 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!
Since there is no indication of other ships, save for drone ships and the (complete) Rebel Flagship, having much of an A.I., this may make your ship the Good Counterpart of the Rebel Flagship. Plus, your ship's 30 hull points exceeds any other ship in the game — even any individual phase of the Rebel Flagship. Your ship is really the only ship that could go toe-to-toe with the Rebel Flagship and actually win.
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.
At first the Rebels consisting of humans only and hating every other race could just be Fantastic Racism, but it may have another explanation. Most players choose to have the other more specialized races over humans, to the point where they may even dismiss humans and replace them. Now imagine you’re a human who’s worked with the Federation for years, only to suddenly get laid off and replaced by a mantis or a slug. No wonder the Rebels have so many supporters.
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?
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.
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.
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.
Despite being primarily meant to be used on your own ship, the Repair Bomb is unable to charge during combat when an opponent is using Cloaking.
Finding the hidden Crystal Homeworlds is a treat, until you realize the rebel fleet is still pursuing you — YOU led the rebel fleet here.
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)?
When you clone a killed crewmember, sure you have a fresh copy of that person, but presumably, the original body is still dead and the original mind gone from existence.note Although your interpretation may vary based on what you believe happens to someone after they die.
