I can't help but think I would've preferred having an entirely original character as the protagonist if I'd known where the plot would go in the later chapters. The only really interesting thing they did with the Amanda/Ellen dynamic was Marlow's line during his attempted mass sacrifice that "if your mother was here, she'd be helping me." That actually gave me pause, and I appreciated it. Otherwise, Amanda's arc is "she's trying to find out the truth of her mother's disappearance, then she does." Then it's over abruptly. An original character might've allowed them to do more.
Speaking of Marlow, what's with his last line? "I loved my wife, and I killed her." Huh? The chestburster did that. If he was blaming himself for her death they could've done a lot better than introducing that idea with his last line. It doesn't help that the delivery of the line is off, but whatever.
When you first meet Waits in person, he accuses you of messing up his trap. How so? The explosion still hit the alien, it just didn't kill it. What, was the alien going to be standing right on top of the bomb if you hadn't walked in?
Amanda doesn't even react to Samuels' heartfelt last words ("I wanted you to have closure"), what's up with that? And was that sentiment programmed? Samuels was clearly the Bishop of this game, but underdeveloped just like everyone else sadly. They could've done more.
I'm not sure if the scene where you interface with Apollo was meant to be comedic or awe inspiring or a mix of both. The reveal that the huge dome is actually covering an exact clone of the Mother system from the film makes it seem like Seegson just stole the tech from Weyland Yutani and covered it with a fancy dome mostly for show, but the swelling music gives the scene serious grandeur. The fact that you've already gotten a peek at a recreation of Mother on the Torrens takes away from the scene too. The scene makes me wonder where Mother's actual computing hardware is if it takes up so much space, but this is also the universe where human-like AI is common and contained in the space of a human brain, so I should probably stop wondering.
The idea of the nest was fantastic, going there was great in gameplay and in presentation (the sound when the whole thing comes violently awake is just incredible, and the scenario is sandwiched between runs in the reactor core, which is amazing aurally as well; it must be overwhelming with a good sound system), but it really makes you wonder why the station wasn't overrun before. Communicating the scale of the station and the relative scale of the alien threat is a huge, maybe impossible challenge for a game constricted (mostly) to a single perspective; the film was intimate in scale for good reasons. Cutting back on the number of aliens implied to be aboard could've helped, and the station doesn't need any help going straight to hell anyway once it starts falling from orbit.
I also think it might've been beneficial to mark a certain alien as "your" alien, to reinforce the idea of it learning your tactics and present the idea of it hunting you specifically as a justification for it always being nearby. I'm imagining an alien scarred by an attempt you made to kill it, with a vendetta against you. This could even create a twisted familial relationship, to give some depth to the Amanda/Ellen dynamic. Perhaps it's not even hunting you to kill you, but recognizes you as an ideal host for the next queen after you destroyed the nest (the weird ambiguity of the alien reproductive cycle is another problem others have mentioned, I wonder if it was the insistence that they use only material from the first film as much as possible that caused it). In any case, the aliens really seem to see Amanda as special in the last part of chapter 18, where they watch patiently as she sets up the detonator. Having like 5 come at her at once was pretty laughable, just an absurd escalation. The detonator being a clone of the one in the film was also a badly chosen homage; that one caused a nuclear explosion, this one blows up the locks tethering a single ship, but they just had to have it I guess.
Amanda tearing out of the wall of an alien nest (without being impregnated to boot) was just bad, verging on bad fanfic territory. You don't break the fundamental rules of an established universe like that, I mean, come on. If an alien traps you, you're not getting out without help, period. It's no fun if an ordinary person can overcome it, the fear is gone. I was confused as to whether she'd been impregnated too, it was just a poorly conceived (ha!) plot point all around.
And the ending's dissatisfying. It's funny to see how quickly Amanda goes from wanting to save the survivors on Sevastopol while on the Anesidora to just trying to save herself, with every single other soul dying horribly by the end, most completely helpless. Again, scale is a big issue. Communicating the plight of the survivors was not the game's strong suit. Really, every major character in the game had a truncated arc, and it's just too bad. They made surprisingly poor use of the cast they introduced at the very beginning, and while Amanda gets her closure (kinda sorta maybe), we don't.
Oh well, really enjoyed (and am still enjoying) the game, I just had high hopes for something that openly expressed its desire to stand shoulder to shoulder with the film, which is such a seminal work. It can't, but the strength of its gameplay is a very pleasant surprise that makes it strong in a completely different kind of way. I won't go into that since the purpose of this thread seems to be more about writing discussion and this post is already more than long enough.