You turned on anon a long time ago and I forgot to ask. Sorry! I just wanted to ask what is the proof that Gendo SAed Rei? Here's an interesting thread by the way. I just wanted to know your thoughts.
Hi, thanks for your question.
This has been a rather contentious topic for a long time in the eva fandom. The thread you linked started in 2009, but I'm sure this was being discussed before then as well.
Before I get into anything else, I want to point out that this is an evageeks thread. The evageeks wiki is somewhat useful for things like trivia, but it is not a good place to go to for in-depth analysis of the girls and women in eva, their trauma, and how that relates to gender. Evageeks is rather misogynistic and clownish.
I have to assume that by "proof" you don't mean explicit dialogue, since you're talking about Neon Genesis Evangelion and asking an analysis blog about it. Analysis is about reading between the lines, yes? But I suppose it's worth bringing up that Ritsuko does mention the abuse pretty explicitly in a draft of episode 24, if that's worth anything to you.
To me, it's obvious that Gendo was sexually abusing Rei. The fact that she's a teenaged clone of his dead wife is suspect enough, but let's dive deeper.
The scene in episode 5 where Shinji tries on Gendo's cracked glasses in Rei's apartment is pretty solid evidence. The glasses represent Gendo's worldview -- his gaze -- and the fact that the lenses are cracked, distorting the sight of the wearer, signifies that Gendo's worldview is very warped. The first thing Shinji sees after putting them on is a naked Rei, too. Shinji then falls on top of Rei, accidentally grabbing her breast. This mirrors Gendo's purposeful action in end of eva. The cherry on top of all this is that Shinji violated Rei's space -- he not only walked into her apartment when he believed she wasn't home, but was also snooping around in her room! He could've left her new ID card on her bed or dresser and left. This is interesting when you compare it to Toji's attitude towards Rei's space in episode 17 -- he's a bit weirded out by Shinji's willingness to just barge in and clean up while Rei isn't home. Also, in the scene from episode 5, you can see shoe prints on the floor in the apartment that don't look like they come from Rei or Shinji, so make of that what you will.
Another tidbit I want to mention is that there's a scene in episode 23 where a bunch of tiny Reis pop up out of Shinji's hand while the angel is attacking. In the ADV dub, what the tiny Reis are saying is "Ikari, it hurts!" I'm not sure what the Netflix dub dialogue is, and I doubt this dialogue is indicated in any subs. If anyone reading this speaks Japanese and wants to weigh in with what the tiny Reis say in Japanese, please do. Being that the later, more psychological angel attacks dredge up the pilots' past and ongoing trauma, I find this relevant to mention.
There's also the many scenes of Gendo gazing at a naked Rei throughout the series. Most notably in episode 15, which also shows Ritsuko glaring angrily at Gendo in jealousy while he does so. Later, in episode 23, Ritsuko says that she lost to "these dolls," meaning Rei and the clones. Lost in what respect? In what ways are Ritsuko and Rei different? Well, Rei is younger -- the same as Ritsuko was when she first met Gendo. Also, even though Ritsuko is thoroughly traumatized, she still retains some semblance of an ability to say no, and conceptualize the consequences of saying no. She had a life before Gendo. Rei has not experienced a version of life without Gendo. In episode 5, Rei asks Shinji why he doesn't have faith in Gendo, to which Shinji replies that he doesn't trust him. The "faith" vs. "trust" distinction is pretty consistent throughout English translations, and Rei's usage of "faith" indicates the god-like power that Gendo holds over her.
Ritsuko inherited the tripartite division that plagued her mother: that of woman, mother, and scientist. She views Rei as sexual competition (I hope it's not controversial to state here that Ritsuko and Gendo had a sexual relationship? Also there's that part in episode 24 where she basically says that he's raped her), which is "woman." She's one of Rei's caretakers, arguably spending more time around her than Gendo, which is the "mother" part of it. Finally there's the "scientist" part -- Ritsuko is a scientist and Rei is her test subject. There's a scene early on in the show that's rather striking. Rei is bandaged up in her underwear undergoing a full-body scan. This procedure is supervised by Ritsuko, who coolly converses with Misato as if none of this stuff with Rei is happening. Despite the fact that Ritsuko's the one supervising it! Not an ounce of concern or compassion. Because that's what abusers do, they divide, conquer, and pit their victims against each other.
It's worth noting that if you look at the Gendo-Ritsuko-Rei dynamic as a warped version of a nuclear family, it aligns very well with what is known about families where the daughter is being sexually abused by the father. Typically, the mother (Ritsuko) in this situation will only tolerate the abuse of her daughter if she is also being abused or if she feels especially powerless. Both of these describe Ritsuko, who thinks of Rei in much the same way Naoko thought of her. Naoko was sleeping with Gendo and being manipulated by him, too. Also, a lot of people in that thread you linked deny that Gendo was sexually abusing Rei because "he thought of her like a daughter." They point to the line in one episode where Gendo says that if his and Yui's child is a girl, they'll name her Rei. But sadly, fathers do sexually abuse their daughters. Even ones who are biologically related.
It's horrible -- nobody wants to think of it, but it's an uncomfortable truth. For far too many men, the definitions of "daughter" and "lover" are not mutually exclusive. I believe that "incest" as a term applies to Gendo's abuse of Rei because he's in a caretaking position, Rei thinks of him as a caretaker, and carries all the baggage that comes along with having an abusive caretaker. Nobody with more than 2 braincells to rub together would say that the Nanami-Touga thing in RGU isn't incest simply because they're not biologically related. Rei's afraid of being abandoned by Gendo, works hard to figure him out, why he treats her the way he does, why she was created, and what to do with herself. Shinji and Rei's Gendo-centric angst are two sides of the same coin; the edge that separates the two is gender.
With all this in mind, the structure of Gendo and Rei's relationship heavily gestures towards the familial. The evageeks users in that thread correctly observe this, but they allow their own naive assumptions about abuse to prevent them from taking the next logical step in their analysis of the show.
Lastly, a major part of Rei's character is her relationship with her body. Any type of trauma and abuse, but especially sexual abuse, has a nasty habit of disconnecting victims from their bodies. A major theme surrounding Rei's character is her body. It's so overwhelmingly obvious that even the dullest viewer would pick up on it. Rei spends a decent chunk of her screentime naked, and her status as a warm body is relevant to Gendo's plan for 3rd impact (he needs Rei because she houses Lilith's soul in a physical form -- this was his own design), the dummy plugs (which run off her decision-making process), and Gendo's abuse of her (she is literally a clone of his dead wife, whom he spends the entire show trying to reunite with).
I hope this answered your question!