OK, I feel we are getting sidetracked here. I'm not arguing your vision here, what I'm trying to point out are some mistakes, as I see them, in its delivery. You are creating a product here. Goal of every product is to reach as broad audience as it can. What I have seen in your product so far tells me there is a good potential to be a great product in the end. There are some design choices that I feel are mistakes 'cause, in my opinion, are not necessary or there is a more elegant way to reach the same goal. Humans are opinionated, judgmental little shits by design but, in the end, they are your customers. You will do yourself a huge favor by not antagonizing them when it's not absolutely necessary. I'm aware of your objective limitations, financial, hardware and timewise so let me try to suggest some small changes that, I believe, will make your product enjoyable and entertaining to a broader audience. Those changes, as you will see, shouldn't change your vision of the story progression (too much/at all).
From the start of the game leave everything as it is until we arrive to Hive scenes. Believe me, triangle flashback is a nice detail but is not enough of a hint. Yes, you are placing it (almost) every time MC "meets" one of the girls (for the first time) but, it is too early in the game, for some of players, to catch on that it's a strong signal to interact with that person as much as possible. So in Claire dialogue, when she asks MC for a dance, after his response "I would love to, but I'm supposed to meet someone." change her response from "I know." to a bit direct one, somewhere along the lines "Yes, nice to meet you." or something along those line.
Later on we come to "no choice" action choice, first choice in game that player can make. People hate such things, being presented with the false choice. Since there is no choice but to go through Claire ladies' room scene don't present players with the action choice that penalizes them with Game Over, it serves no purpose but to get some people pissed. Believe me, there aren't many people who will find it funny, if that was what you were aiming for.
As the story unfolds insert a triangle flashback when MC "meets" Sydney for the first time, right after this screen.
This way you are keeping consistency. OK, maybe there is a reason for Sydney not triggering a flashback, if so you can just disregard this.
In dialogue with Hauer we come to the first problematic dialogue choice (second player choice of the game). If you are offering players to have MC feel "tricked", don't make him a douchebag through consequent dialogue lines. Players have a tendency to identify with MC, you are essentially insulting them for making a wrong choice. Better not have a choice if, once more, this choice serve no purpose other than to aggravate players. If your intent with this choice was to portrait MC as a blunt but able to recognize his mistakes, and therefore you insist on leaving this choice, think about better dialogue after it, maybe somewhere along the lines of Hauer apologizing for making MC feel that way and saying that it was not the intention, essentially playing it as unfortunate misunderstanding.
Second dialogue choice is not a problem by itself but I feel it also should be mentioned. If player doesn't choose "Government" he misses (maybe important) detail of Hauer's mistrust towards "old ways". Maybe there shouldn't be a choice at all.
Third dialogue choice (fourth player choice of the game) would not be a problem if previous choices weren't antagonizing to players. You can easily mitigate this "problem" by making the choice between directly or jokingly accepting the job with button labels written as "Yes" and "No (joke)". By this time is obvious enough that MC will accept the job so, if you feel there is a need for this dialogue choice, at least make it a bit lighthearted one.
Once more i feel there should be a triangle flashback after MC see Spider for the first time, right after this screen.
And once more, it's just for consistency reasons but, as with Sydney, if there is a reason why Spider doesn't trigger a flashback just disregard this.
To recapitulate. Current situation with your product is that first choice of the game can piss off some players, second one can insult them, third can make them miss a (significant) story detail and the fourth one is just vague, but will be negatively received after previous choice experiences. Those lucky players that, one way or the other, go past those initial bumps can enjoy a very good story all through to the end of current update. My suggestions to you were made in effort to make the number of those players bigger. I hope you will take them as they are, just honest suggestions, and will at least consider them.
Best of luck in future development of your product.