I've heard from some who I've been chatting to that the reason Rei and Shinji's relationship turned out the way it did in the third and fourth film was because it was meant to recreate the Oedipal Freudian undertones of the original series. And that it further shows why her connection to him was overall a bad thing for both characters. To quote:
Shinji exhibits as much an oedipal attraction to Rei in Rebuild as he does in the original. This he says in 2.0:
"I feel safe in the entryplug. It smells like mother... or Ayanami."
Aside from the connection to his real mom, the thing about Rei's attraction being maternal is because Rei is willing to erase herself for him and doesn't demand him to grow or fight. She represents a mother of the same age to Shinji. A safe place to be. In Rebuild they even added the "Ayanami clones are programmed to love him". I can't think of a more obvious maternal metaphor.
Anno believed himself to be fixated in the freudian oral stage. He believed he looked for a mother in women, and he hated that about himself.
That's what Shinji does. He looks for a mother in women. A safe place to be, where he is never challenged. A mother he can sleep with.
Rei being willing to erase herself for him and not demanding him to grow is not a good thing. It is terrible, actually. This is why Asuka says in Thrice "that child doesn't need a lover, he needs a mother".
Kaworu is basically the same thing but in male. A father of the same age as him. Notice how when Kaworu realizes Shinji has grown he is saddened. Because Shinji won't depend on him anymore. Same applies to Rei. He won't need Rei anymore as a maternal refuge.
Thrice Upon a Time is basically EoE 2.0. A more palatable version of it, in which the characters face the same struggles but this time they don't fuck up:
-Shinji can snap out of his depression and apathy.
-Ritsuko actually shoots Gendo, and doesn't depend on her mom (the MAGI) to go against him.
-Misato hugs Shinji, and is to him the mother he needs, instead of the weird thing she did in EoE. Her ultimate sacrifice and death are not in vain.
-Shinji this time is capable of showing true love to Asuka, save her and sacrifice himself for her (and everyone else), instead of trying to cling to and look for a mom in her (which Asuka will never be for him, that's the whole point of her relationship with Shinji).
-Just as it happened in EoE, Shinji takes away from Gendo his two moms, fulfilling the oedipal narrative: Yui (Unit-01) and Rei ("Ayanami, I'll take it from here").
-In the end, Shinji has a conversation with Adam and Lilith, his two "parental figures of the same age", Rei and Kaworu, and moves on from the comfort of being with them, just as it happened in EoE. Only that this time he saves both of them.
Anno's Evangelion at least, is about that. That's the core of the story he was trying to tell, and these are his words: the story of the oedipus complex in a multilayered structure.
This multilayered structure is basically that almost everyone close to Shinji is a mother or a father figure to him:
Gendo, Misato, Rei, Kaworu, Unit-01, Kaji and even Kensuke and Toji become father figures in Thrice. The only character who is never supposed to become a mother figure, even if he would like to, is Asuka. Asuka is inserted in her own female oedipal structure, and she is the one that actively refuses to be Shinji's mother. She symbolizes to Anno the woman who won't submit to his "oral stage" whims.
The movie gave resolution to Rei's relationship. That resolution was that Shinji did not return her feelings and helped her move on. The sole fact that he returned Asuka's feelings is already indicative that, at the very least, he wasn't really in love with Rei 2 back then. The one he really loved was Asuka.
Rei's relationship resolution is the same as Kaworu's: he tells her to go live her life, holds back from her the fact that he doesn't intend to return (he even lies to her, but he doesn't hide it from Asuka), they hold their hands and Rei exits the scene through a shutter. Just like Kaworu.
Gendo ultimately reunites with Yui (to sacrifice themselves, though) because Thrice is EoE if everyone did the right thing. Gendo also gets his redemption in Thrice. But Shinji does seize both Unit-01 and Rei from him at first. The oedipal framing is symbolic, and it doesn't overcomplicate anything. It's a son seizing his mom(s) from his father, it's pretty straightforward.
Man, all that really frames the relationship, something that I found one of the strongest aspects of the Rebuild saga, in an extremely negative light. And yet, I'm not sure anyone can really refute it. Especially considering that her becoming her own person separate from Yui wasn't in fact the point of her character, as her feelings towards her was purely maternal, nothing more.
Rei is a clone of Shinji's mother, and was created to fulfill a specific purpose. This isn't some vague allusion like it is in the OG series, but an established fact. The two ending things amicably on a good note works best for them both.
Rei was never built to last beyond her intended purpose.
Rei's journey has been less about forming a separate identity from Yui Ikari and more about becoming independent from Gendo. She was built as a tool, a catalyst for Third Impact, and her story arc has been about becoming something, someone more than that. None of that changes the fact that she shares the blood of Shinji's mother, and the maternal, nurturing influence she has on his character is a key factor in her relationship with Shinji. If you see them becoming something beyond that, then that is your opinion, and not one shared by Anno or the majority of the fandom.
I didn't say "rest;" I said "most." Stop playing the victim. Your opinion is unpopular, deal with it.
The Rebuilds aren't about developing relationships, they're about closing them. The Rebuilds are Anno's farewell to the characters that defined most of his career. Shinji and Rei's relationship was significant, but not in the way that you expected. She, once again, serves as a catalyst for great change throughout the world, with them both playing into Gendo's plan. Their final moment together was exactly what Anno wanted to say: goodbye all of Evangelion.
Also, this...
as there’s no other Ayanami but her
...is hilarious.
Anyone here have any rebuttals to such compelling analysis? I don't think anyone should be a fan of the relationship between Rei and Shinji in Rebuild given everything outlined. And that's extremely insulting to me, but I can't refute the evidence shown.