The Unplanned Variable is named so because the universe according to Scientism says that everything is predictable. However, the Player can choose to be anything they want to be and do (almost) anything in the setting. They are, literally, the only people who have free will in the video game.
Speaking of Scientism, Vicar Max's religion is partially right because the vast majority of people in a video game don't have free will and are only able to interact within the confines of their programming. His description of the universe as an elastic rubber band that can be stretched by people (players) but not break is a pretty good description of a well-designed roleplaying game.
Scientism versus Philosophists is a fairly decent description of people who believe in a Determinalist universe versus one governed by Chaos Theory. They are both scientific models of the universe that have been sometimes used by (and explained with) religious models. The irony being that quantum physics means that both are right to an extent.
Why are you a Working-Class Hero with such lame backgrounds in character creation? Why not someone awesome from the start versus a convenience store clerk or bartender? Phineas said that there are a lot of great minds but didnt say all of them are. And he also was quite unsure if the thing he used on us worked. We also find out a lot of previous subjects died. So he chose us for the experiment because he was like, Oh, a tossball team mascot, saving colony wont fail that much if we lose him, right?
Why is everyone so gorram stupid in the system? That's because the two colony ships were segregated with the geniuses, engineers, and scientists being located on one of the ships (Hope) while the corporate leaders, laborers, and middle managers were on the latter. There was some overlap but the loss of the Hope meant that the colonists were left with roughly seventy years of corporate rule as well as minimum education outside of Byzantium. Even the best educated people also were encouraged to pursue what was profitable and pleasing to the Board, rather than what was genuinely helpful to the Halcyon colony as a whole.
Why is Ellie a Nominal Hero only out for number one? She grew up on Byzantium where everyone is encouraged to be a Rich Idiot With No Day JobSpoiled Brat with Fantastic Racism to the poor. The irony is that Ellie is actually nicer than the average member of her society and considerably less bigoted even if everything she's doing is an elaborate five year-long teen rebellion.
Felix's chip on his shoulder regarding the Board makes a lot more sense when finding out that he's Chairman Rockwell's abandoned illegitimate son.
Even before Max realizes what an ass he's been, he can give Felix advice on how to have a better mean left hook quite earnestly. Max has said before that his parents called his poorly-masked penchant for violence "violent enthusiasm" (which he admits to not having controlled very well during his youth), and the first weapon that he mentions being good with when you recruit him is a tossball stick. Tossball is one heck of a violent sport. As if that wasn't clear enough, if you head over to Byzantium with Max at your side two Byzantines will comment on how your friend seemed familiar...Perhaps an old tossball player? Yeah, Max also said he played tossball in prison, but from the sound of it he was probably a tossball player during his youth! There's a reason he's got a "mean left hook". And it's pretty cool that this becomes his bond with Felix.
Why are the worlds of the Halcyon colony so half-assedly terraformed? Because they only have half the terraformers they were supposed to get, because the Hope got lost in transit with the other half of the allotment. The combination of this and the Hope also having the scientifically-minded people who would know where best to drop the monolithic machines also means you have nonsensical things like dropping one on an asteroid. Imagine someone as moronic as Reed Tobson in charge of terraformer distribution: "It makes breathable air, right? Drop it there, it may have valuable minerals."
Zero Gee Brew is a Stealth Pun. Gravity is a term used in beer brewing, generally, the higher the gravity, the higher the alcohol content, which makes sense as to why Spacer's Choice would give Winslow a hefty (for them) discount - it's not actually beer.
Since this is an Alternate History where William McKinley never got assassinated, thus Theodore Roosevelt never succeeded him and formed the trust busters, it only makes sense that getting the best ending in the game involves going by his most famous philosophy: Speak softly and carry a big stick. Sure, you're free to pump the other guys full of iron, but doing so too much might leave you without friends in high places when you need them. You're also free to just talk your way out of any situation, but getting the best ending means killing at least one person (Graham), which is easier to do if you're packing some serious heat. Thus, it only makes sense that getting the best ending in the game means speaking softly when you can and putting that big stick to use when you should.
It may not be that there's no God, so much as that said God isn't the Architect. That the Universe isn't planned or structured, and that its God isn't the planner, but rather something else entirely (For example, instead of a bringer of order and enforcer of hierarchy, the universe's god is actually a being that more closely resembles a hippy)
Nyoka's best friends committed suicide possibly a couple of days away from rescue.
Just how many people were killed by taking "Early Retirement" in Byzantium?