MASSIVE SPOILERS for Ascension below. You've been warned. Like, seriously, don't even read this if you haven't seen past Episode "2".
Also, if anyone who's familiar with me and isn't hostile has been worried, no I have not been alright. I'm going to take a break from my personal problems to sort this whole thing out for people and address most of the so-called "plot holes", as the plot is actually quite simple:
Life Boat for Humanity
The USS Ascension is, in fact, an actual "life boat for humanity". The ship is a real, functoning ship. This is part of the trick and how the project was able to (not) "get off the ground", as for all intents and purposes to the uninitiated the ship was actually constructed and for all anyone would know was actually launched. IIRC, the crew "woke up" after their supposed launch.
By the way, the years this takes place in and Christa's visions are no coincidence, because if you're worried about the President knowing, well...1963, hello! Remember that the corporation that lauds itself as in charge of this project on Earth basically kills everyone that it is done with, something clearly and repeatedly established. Each of the events she mentioned are intentional, and leave important clues as to the Ship's true purpose as well as any lingering questions as to how such a project could be gotten away with.
This is where I'm not understanding some of the confusion; clearly this would have all been entirely necessary even without the revelation about Christa (and possibly others') and her connection with the Ascension.
This is a generational ship, meant to be in Deep Space for quite some time. The main conceit, then, is that the population simply isn't going to be able to make it without this. According to what the show is telling us, the project's developers found that you can't just take a ship and put people on it. You have to make people who can live on that ship. Thus, the breeding creates people who are capable of surviving on the ships first. This is a "generational ship" in more ways than one; humanity has to be better adapted to that environment if it is going to be able to survive in it. It's going to be interesting to see what happens to Stokes.
This also handily explains Christa: She's so adapted to the ship itself to the point that she can "feel" it, as stated "like a skull beneath skin". She isn't "psychic" so much as she is so attuned to the environment around her to such a degree that she could not only tell where they were (their actual position in space), but she could tell there were surveillance cameras on her and something wrong with her milk. This isn't "magic", nor is it exactly "psychic"; this is simply a science fictiony stretch of human spatial perception. She has no psychokinesis of any kind, either; merely a connection to the ship's machinery that allows her to act as a conduit to its "ocean". Please remember, Water Reclamation was adapted into a beach; it wasn't built that way. There's probably some kind of deuterium processing going on there.
This is also why Harris keeps repeatedly emphasizing the point of how the whole thing is supposed to be this kind of closed ecosystem, because it actually is. When he claims that Christa and the ship are a part of each other and that she is the heart of the ship, he's meaning that rather literally.
This is also the real "Rubicon", or point of no return: The crew can no longer adapt without the ship, they need it to survive now.
It has become appallingly obvious that our technology has exceeded our humanity.
Ergo, accelerate humanity so that it can catch up to our technology. They developed some kind of FTL or "Jump" drive that no-one could operate yet. This kind of thing has real-world precedent: We've developed vehicles that no-one could operate yet before, and in the 60's no less. No one could really drive it as the mental strain of operating the vehicle was just too much for people at the time. I suspect that modern ubiquity of controller interfaces would change that should anyone strap in one of those today.
Presumably, the TCS Corporation has been lied to about some kind of eugenics in order to get them to have even funded the program to begin with, giving them the promise of super-people in order to get them to play along.
There's an incredibly good reason you would need to take it all this far: Math.
Math controls everything about this project, and in fact everything about the show's mechanics. The outcomes of calculations are the whole point.
To start, the simulated star field was calculated out in advance. That's all well and good, but at the time astrophysicists and their ilk were still (and are still) sussing out all of the various forces that make up our universe. Hell, Black Holes had only still been predicted at the time of the project's launch. This establishes, though, that regardless the science of the project was soundly structured surrounding predictive modelling. Remember the selective breeding program? The birthing computer is real, and it is obviously running a predictive algorithm. This is the technology that they had available to them during the project's creation. Also, remember that whole part about navigation? Yeah, digital computers aren't going to do the trick when staring down quantum mechanics. The crew itself will eventually be the ship's computers, doing manual quantum calculations.
You see, there never was enough time.
Let's go back to Christa's visions for a moment, then: Kennedy (political problems/political power/hand wave about Presidential involvement), Middle Eastern conflict (Resource wars), and 9/11 (religious fanaticism).
How do these play out on the USS Ascension? Not one murder in 50 years (discounting the entirely apolitical sabotage, oh well) with incredibly tame power plays, highly sustainable resources that keep on sustaining owing to technological advancement and societal structure, and - how has no-one noticed - a complete lack of religion of any kind. There are references to Greek mythology and they know that the Bible exists obviously, but how has no-one noticed the complete lack of any church, any obvious religious under- or overtones?
Contrast this with what happens outside of the ship: We have the TCS corporation milking the project's innovations for money, we have the corporation killing people and expecting to make some kind of superhuman out of it for power, and then we have conspiracy lady talking about some kind of hippy woo-woo "Star Child", which is clearly some kind of religious fanaticism. She wasn't a part of the TCS corporation; she was a cultist. Why do you think she was after their DNA? Why do you think Ascension crew member bodies were cremated immediately upon death?
Harris's father knew this would happen. It was predicted! That's why I say there simply wasn't enough time to do anything else. The 150 year mark is intentional, too. How do people not remember the oft-cited supposed 150 year mark for remaining oil?
If predictive modelling is in the project's foundations, then that also means that the project was created because (Cold War or not) Earth is very likely doomed. Not only from the Cold War/Power conflicts, but from resource depletion or religious fanaticism. The numbers were run, and the project needed to happen.
While there's always the off-chance that the discoveries made on-board Ascension might save the Earth itself, it seems to be enough of a bet that the planet is doomed, like, bad.
Also, Christa's claim of "there's no life there" could be in reference to her being able to calculate things like the presence of a Black Hole, or maybe she can just crunch the numbers to be able to tell where there is and is not actually any life. With FTL/Jump/whatever ability and with the lack of available science in the 1960s, this ability allows her and others to be able to go find a habitable planet without getting everyone on board stranded or killed.
Ascension is a Life Boat for Humanity
Literally. The ship is space-worthy, that's an actual ship there. How was that not glaringly obvious? There's no reason for there to be an entire ship with the entire hull if the thing is only a simulation; the damn thing is in a real fortified underground launch hanger with pits you can casually shove people down and everything. The ship is real, the hangar is real, the thing can launch.
However, you don't launch a life boat until the ship itself is actually sinking. You build one just in case. What I suspect is that although the likelihood of doom has been calculated to the point where it justifies the project's creation, there's still a chance that it doesn't need to be launched. Ascension exists "just in case", but in order for it to exist at all there has to be a crew that is capable of manning it. The ship will actually launch when it is needed or ready. The whole thing is generational; the development of people who can see the project through, including Harris himself. It's been planned for the extremely long term.
I swear to you I heard a car horn beeping at him while he got away. I'm pretty sure the guy we saw at the beginning was picking him up.
What about Lorelei?
She was going to kill everyone or otherwise get everyone killed. Seriously. Also: Caprica. She was obviously tied to whatever that machine is down there in water reclamation and quite possibly even uploaded herself into some computer somehow.
Despite their lack of colour monitors, the MRI - a complete functional MRI - we see on-board the Ascension is more advanced than what we have out here in the real world. What if the ultimate purpose of this device is to be used as an interface? I bet you Lorelei is actually in the ship somehow. That would explain the situation with the video of her and the captain. She isn't a hallucination...and I don't think she's anywhere near anything innocent nor good, either.
Basically SyFy made a prequel to SG1/SGU, Firefly, and Caprica altogether. The show is going to get triple-cancelled...Or maybe not, seeing as how it could easily slot into any of those shows, maybe the point is to re-build their TV catalogue with something like them? Ascension is basically one big apology and one re-incorporation of SyFy's back catalogue (including Firefly, which I know wasn't its fault).
Like those shows I mentioned, this show was really smart. Here's to hoping lack of viewer comprehension doesn't justify some kind of executive "viewers are morons"-based "I told you so" and get wrestling put back on Fridays. I have a sneaking suspicion that it was moved to the death-slot because we're going to get Sci/Sy-Fridays back.