Rei is a monster. People forget this and act like she's human. She's half alien, half Shinji's mother. She is no different to Kaworu. If you think she deserves a good ending then you missed the entire point of Rei. She is not human, she is not a child. She is a meat suit for an Angel to walk around in. Shinji clinging to his mother's autistic clone, with none of the personality or soul of his mother is not a good choice. Putting aside any of Anno's personal issues. Would you think it's a good idea to fuck your teenage mother with the soul of an alien in her? There's no good in any of that. Shinji picking Rei is either incest or xenophilia. Neither is picking a real human woman. And one of Eva's original core messages was "Human relationships are hard, they hurt and you have to open yourself up to that hurt or you never get any of the good parts". Rei is not human, Rei can never be human. She is picking your 2D incest waifu over a 3d woman. When Shinji picks Rei over the rest of humanity he is making a bad decision. And then when we see the effects later, Rei is just mass produced any way. She's still an alien, she's still a clone. His attachment to the fake doomed the real. And Eva has always said picking a bad reality is better than picking a comfortable falsehood. The fanbase is so autistic at this point it needs Asuka to scream it at you from a fan festival movie.