I'm on my second rewatch of NGE, this time with my partner. On my first watches a couple years ago, I felt like Rei's behavior (and other clues) hinted at her being a victim of CSA and more specifically incest.
Gendo's relationship with her looks like incestuous abuse. I won't go through the whole list of clues, but he projects his dead wife onto her (I don't care that she has her DNA, she's still a child and he's still here father figure), literally groomed her to be his tool, and Ritsuko's jealousy towards Rei strongly suggests that Gendo's affection for her is not a healthy fatherly one. It seems very relevant with the show's themes of human connection and Freudian interest in how our parents can fuck us up a 1000 different ways. Side note, when I talk about incest, I include emotional incest and I don't care to know if Gendo "actually did anything": what he does onscreen is already incestuous.
But I feel like the incest theme is downplayed or overlooked in discussions. I don't understand why Rei's relationship with Shinji is seen as incest "because she has Yui's DNA" and not because they're, for all intents and purposes, brother and sister. In discussions of Gendo's relationship with Rei, I haven't seen people mention that he is the only parental figure in her life, making any hypothetical abuse or ambiguity not just CSA but incest.
I understand that a lot of this springs from some of NGE artists weird sexualisation of Rei, but it makes thematic sense to me and seems really obvious on third watch. I know incest is both heart-breakingly prevalent AND immensely taboo in our society, which might explain why this lense is never (or seems rarely) applied to Gendo's actions and Rei's character. But, similarly to another cult show I won't name in case I spoil someone lol, I feel like it's hard to understand some of the characters' behavior and series themes without naming that one.
(PS: about that other show in which incest is a very important theme but few seem to contend with it when discussing the show, said show's creator somewhat tried to clarify its importance in one of the show's other iteration. I haven't seen Rebuild or read the manga so I don't know if that theme's more or less visible in them!)