Sorry, what? 1) How exactly does "Lilith moves parts of her body around" correlate to "Lilith sends visions of Ghost Rei to people"? 2) And why would Lilith be sending visions to Shinji before he meets Rei, pilots an Eva, or even sees an Angel? 3) How does Lilith reap the souls of those who died before Third Impact, like Misato and Ritsuko, if she has no ability to bend time? 4) Moreover, why do you even have a problem with this hypothesis in the first place?
1) It correlates because it shows that Lilith and her considerable powers aren't out of the picture while Lilith's soul is in Rei.
2) In case you haven't noticed, Lilith has at that point incarnated herself in a body that is a copy of Shinji's mother, is currently loyal to Shinji's father, and has Shinji's mother in the other half of her original body. She has plenty of relationship to Shinji already, even before she meets him.
3) Why does she need to be able to manipulate time to do that? Manipulating souls, gathering them, taking them into oneself- that's just what Seeds do (even Seeds without souls themselves!)
4) And I have a problem with it because it's like the sort of theory that claims that Shinji and Asuka had sex and that Asuka is pregnant because she says that she feels sick- making a massive upheaval in the understanding of the story in order to explain a minor point that has far more obvious explanations.
What, Rei was scared of becoming a deity, but turns out becoming a deity was actually cool and good? There is zero indication of the latter; the only shots of Rei we get post-Instrumentality are ominous and do not portray her as happy - quite the opposite.
The scenes we get of her persuading Shinji to agree to end Instrumentality
are warm and tender and hopeful; those can't be counted as Instrumentality except with a huge asterisk. I see no reason to think that she's in horrible misery after just because she's not all smiles all the time.
And, yes, becoming a deity generally is cool & good, especially when it manifestly doesn't involve the bad things you were afraid it would involve.
The meme doesn't come from nowhere. Gendo isn't omnipotent; but he is misanthropic, and he is selfish, and he does treat other people like less than dirt. I think "evil" is a fair characterization.
He can and does. Also, sounds like you concede to him manipulating Rei.
He does. "Running away again?"
He manipulates Shinji plenty. His ultimatum ("Pilot or leave!"), as well as bringing out Rei in bandages, is one example of this. Same with how he makes sure to praise him very sparingly. Shinji only pilots because he wants his father to notice him. Gendo is aware of this and actively fosters this dependency.
Gendo doesn't have to be incredible with people to be manipulative. He's in a position of tremendous power over anyone he chooses to manipulate, whether that's his son, his foster daughter or the woman he's been grooming since, like, 17 (before he casts her aside to be raped, of course).
It feels very strange indeed having to explain how Gendo is manipulative, because it's just such an obvious part of who he is as a character - it's like making the case for Shinji being passive or Asuka being abrasive. It's just self-apparent.
Regarding Gendou manipulating Rei:
Most persons seem to assume that Gendou manipulates Rei in the following manner (exaggerated):
"I will take this poor, innocent girl and systematically abuse her and keep her in despair so she'll never get to find the happinness she'd get if only I'd let her be a normal girl, all so I can fulfil my plans using her."
Which has no support except by just outright imagining interactions between them dramatically different from all of the ones we actually see.
When in fact what's going on is:
"Here is my daughter, whom I have given the name I planned on giving my daughter, and whom I care about to the extent of completely breaking my cold facade and losing my shit whenever she's put in danger. Even though
if she dies I can just reincarnate her.
Please however note that my daughter is also the primordial deity who created all life on this planet. I'm really not sure about this deity's intentions- perhaps she'd hate me for what we've done to her. I'll need this deity's power when the time comes. So I'm not going to tell her about that part. It shouldn't be a problem, to be honest. I trust Rei completely, she understands me, I understand her, she doesn't run away from me like my son does."
Which is, indeed, a considerably more bizzare relationship, and that doesn't even get into the mythological dynamics of what's going on in the Terminal Dogma scene.
The tl;dr, I guess, is that Gendou treats Rei-as-merely-Rei with as good a heart as he has (which isn't, again, even close to a good relationship, but it's still treating her with the love that's genuine for a self-loathing freak like him); it's Lilith he's trying to manipulate- and that just by not telling her who she is.
If you have evidence that Gendou groomed Ritsuko, please explain what it is.
Your other examples regarding Shinji aren't really persuasive. I don't see any reason to think that Gendou is expecting to change Shinji's mind by bringing in Rei. I think he's genuinely just concluding that Rei will have to do it, since Shinji won't.
It's the exact same thing he does the other times Shinji refuses to pilot. He shrugs, says something nasty but truthful, and then concludes that Rei will pilot Shogouki, as was always plan A. When Shinji runs away in episode 4, Gendou literally doesn't even do a thing.
The impression I've always gotten, indeed, that is that far from trying to get Shinji to pilot, Gendou is inwardly trying to repulse him. He's emotionally afraid of Shinji and wants
him to leave. Which is why he makes absolutely no effort to get Shinji to stay.