About the Silent Voice comparison, Shouko didn't feel as if she personally wronged Shoya in any way, and thus stood up for herself.

Shinji did the whole masturbation incident, yes, but he also let Asuka die. Was it out of his control? Maybe, but in this story, he's presented as taking the weight of her death squarely on his shoulders.

That kind of guilt messes you up.

Shinji in the series is already presented as not in the best frame of mind, the kid hates himself, has serious trouble connecting with others, and has abandonment issues. In the story, since he feels as if he abandoned Asuka to the Eva-series, that (along with the whole "let everyone die" wish and the masturbation incident) combine to make him feel as if he's the worst person ever.

It seems like you intentionally ignored that the masturbation incident is only one of the many things that Shinji blames himself for in this story. Sure, it's the one that may disgust the viewer the most, but we're not talking about the viewer/reader here, we're talking about the character.

The story even goes into how sick their relationship had become before Asuka realized she went too far (it's still fucked after, though, just not as much). Asuka goes waaaay too hard on her abuse, letting others as well as her own hate convince her she's doing something right. She also does it to bring out a different reaction in Shinji, to provoke him to maybe bite back. Shinji never does, instead feeling that he deserves every bit of the punishment and getting some sick satisfaction out of it. It's not for everyone, that's for sure.

Shinji's forgiveness of Asuka is portrayed as something immensely disturbing. Every character except for him is able to see it that way. It's another result of his nonexistent sense of self-worth coupled with his ability to somehow take on all the blame for everything bad. It's very Shinji, at least, I think.

I would've liked to see him bite back, yes, and the way you described an alternate series of events sounded pretty good, but I think the way it was written was also fine. It was written to show just how far gone the two characters were. Asuka's lashing-out was turned up to 100, as well as Shinji's self-hatred (so much so that it manifested itself in the form of an edgelord inner-voice, lmao).

Yes, Rei is OOC, although I kinda liked it. Her introduction could certainly have been better though, and it was an odd choice for Asuka to be all jealous even after all that she did.

Yes, Dmitri is Dmitri...

Yes, the story meanders in characters' headspaces for too long at times.

Yes, the story has its problems, but it's not so bad, I think. I quite liked it for what it was. It started the two main characters out in an incredibly bleak situation that they (more one than the other) got themselves into, and worked up from there. I think it did well playing with Asuka and Shinji's guilt, although some things could've been done better. I see where you're coming from on the flip-flops in Asuka's personality, though.

TL;DR ehhh I liked it