Alright, I got some thoughts here:
- I read the game's last ending, E, as the "true" or "final" ending here. In that the nature of everything we played through is cyclical, and is repeated continuously through the actions of the player. The final ending brings about a potential for change, or for another player to break that cycle, reviving 9S, 2B & A2 for someone else to make different choices for a (hopefully) better outcome. In that way the characters didn't "die" as such, not in the "truest" of endings.
- Adam fairly definitively died in his fight with 2B, as he cut himself off from the network in an attempt to experience the only one thing he couldn't understand.
- I kind of interpreted Eve as being at least non-binary, if not female? Eve calls Adam brother, but from what I can recall (and I might be totally off here) that Adam never refers to Eve as anything gender specific. The only other character in the game that identifies differently to what you "expect", Pascal, is named so after the philosopher Blaise Pascal, a male. Eve is pretty clearly named from the Bible, in which Eve is obviously a girl. I read Eve & Adam's creation as a rebirth, as the start of a new cycle of life, with them 2 being "mother and father" of that ideal. Sure Eve has a male physique and voice, but that means bugger all in this game.
- My interpretation of the ending you're talking about, with the ark and all the boys, was a little different. 9S seemed to finally succumb to the logic virus in his fight with A2, so from that he was pretty much doomed. I read the text part with Eve using the rocket to launch away from the planet / asking 9S to go with them as entirely played out in 9S' head, some kind of rationale for himself to accept prior to his final death. Was Adam there at all? I can't recall, but he must have been if you're saying that - in that particular case, as he definitely died as mentioned before, that makes it further proof that it's in 9S' head, not actually happening (to me anyway.)
- Pascal, I would argue, is truly dead no matter what option you go with. If you kill him he's dead. If you wipe his memory he is no longer Pascal at all (to the point of being the equivalent of irreversibly brain damaged, shown by selling machine parts of the children, with his name being "Pascal" only because you remember him as such, not because he identifies with the name.) (also, there's the whole argument made through the game about sense of self and memories and whether you are really "you" without them, but that's a whole other tangent.) If you walk away, I read that as Pascal commits suicide, as he's not seen again (including in that final cutscene, which he's in if you wipe him.) No matter what option you choose, you get the trophy signifying Pascal's death.
- Apart from the fact that everyone in the game is mechanical in nature, none of them with reproductive parts, signifying that "gender" is an irrelevant construct (again, a whole other discussion topic, but won't go down that road here yet at least) I kind of read the game as very pro women. Nearly every station of importance as far as leaders, command etc goes, you find ladies. Commander, Anemone, the red twins. The characters that are male are generally either oblivious where others are knowledgeable (9S is ignorant to so many truths, yet 2B(E) knows much more than she lets on, A2 figures it out on her own prior to the events of the game, Anemone is the one who leads the resistance by adapting to machine's being sentient, Jackass is the one observing everything as a whole (her final report at the end)). All the boys give in to their own selfish desires (9S grief, Adam curiosity, Eve (if you want to call male) rage. All the women are smarter about everything, think about the good of everyone else, do the Right Thing (2B passes on what's important to A2 when she knew death was inevitable, A2 despite being a lone rogue still "saves the world", Commander follows her duty to the end).
- I totally get your interpretation of 9S, but I took it to be he has almost a childlike/optimistic outlook on the world that is shattered beyond repair through what happens to his very meaning for existence. He is killed and reset so many times that he doesn't have the hardness of the other characters, so he is "innocent" in the beginning. I guess that's why o found him likable enough - he was more of a child in my eyes than a man, if that makes sense.
Just want to say I hope this doesn't come across as argumentative or shooting you down or anything, I just love this game so much and want to talk to people about it, debating over thoughts and meanings and all that stuff. So thank you so much for commenting back!
What's so good about this game is it's openness to interpretation. While some creators want to craft something for the audience to feel a certain way or think a certain thought, Yoko Taro has said in interviews he wants players to take what they want from the games he makes, rather than tell them how to be affected. My interpretations are one of many, and I'm so open to discussing and adjusting them!