Why would she know that? Shinji was brought back as a last minute backup only because Rei was hurt. He wasn't supposed to be involved at all. If Rei hadn't been nearly killed by Unit-00 berserking, Shinji wouldn't have even come in. Yui might have known Shinji was able to Pilot due to the mother-child link, but in that case why not train him for the next 10 years like Asuka?
Everything after Yui's disappearance, she of course had no influence over. We
know Rei was part of
Gendo's plan, not necessarily Yui's. In fact, seeing as how Gendo seems to have spun his plan out of whole cloth after Yui's disappearance, I would almost certainly say Rei isn't part of Yui's plan, but exclusively her husband's little idea.
And Gendo obviously knew that Yui being inside EVA-01 means Shinji can pilot it; otherwise he wouldn't have called Shinji to Tokyo-3 for that purpose. And if Gendo knew... Yui probably did as well.
Of course she didn't know Gendo was going to use her DNA for Rei. But a Lilith-hybrid clone Pilot was always going to be made, specifically to be the Pilot, since they knew a Lilith-flesh clone with Lilith's soul would naturally be able to synch with Unit-01, the Unit literally carved out of Lilith's body.
That is not why Rei can synch with 01. Keep in mind it goes both ways: Shinji can also synch with 00. Not control it, okay, but synch with it. Also, Rei indeed
synchs with EVA-01; she doesn't control it like Kaworu did EVA-02. There are no hints of her setting her synch-rate at will as Kaworu did. Also, Yui later rejects her; that makes it clear she had in fact synched with Yui. So... Rei doesn't control the Lilithian tissue of EVA-01; instead she really does synch with EVA-01's soul, with Yui.
She can synch with Yui, and Shinji can synch with the Rei in 00, because they're all related. Family... from a certain point of view (
). That is also supported by Ritsuko's comment during the cross-synch test, that Shinji's and Rei's profiles are nearly identical (and hence they can cross-synch - nothing to do with Rei holding Lilith's soul). How that is supposed to work if Yui didn't even know of her, or Rei-I of Shinji, I have no idea, but it seems to me to be a case of typical Freudian mother-child mysticism so prevalent in NGE.
It is entirely possible that a Lilith nephilim would always be made for the role to play in 3I. But that Rei could pilot 01 had always been due to her being a clone of Yui, not due to her holding the soul of Lilith. And Yui couldn't have foreseen
that, that Gendo would use her DNA for the nephilim and thus make the nephilim able to pilot her unit. So it stands to reason her plan was in fact that her actions would make Shinji a pilot. And I do hold that to be detestable and disgusting.
The clone Pilot was always in the cards. You think Gendo wouldn't have known if Shinji was supposed to be the Pilot before that? Or that SEELE would just shrug and let him replace Shinji if he was meant to be the Pilot?
Meant by
whom? Our argument here is that
Yui meant for Shinji to become her pilot; why would SEELE care about that? And hell, the SEELE debriefing of Gendo after Sachiel shows they indeed had absolutely no clue how NERV used the vast funds they have been given. SEELE wouldn't meddle in something as minor as who gets to be a pilot. And yes, Gendo always knew Shinji was a pilot candidate; that is why he recalled him. That doesn't mean he knew Yui
wanted Shinji to be pilot, or if he did know, that he cared. He had his own Scenario, after all.
And SEELE got pissed when they find out about Rei "surviving" Armisael because that made it plain as day what Rei was; before that SEELE probably didn't know she was the Lilithian nephilim.
Fuyutsuki is probably low-key just as big a piece of shit.
As I always point out, at the end of episode 14 he thinks Gendo cares
too much about Rei. Also, he was a MetBio professor. It seems very likely to me he was involved Rei's creation.
If SEELE agents didn't go in and hang her, they probably gave her the rope to do it with.
Well, metaphorically speaking as well, probably. Asuka was snatched up as pilot basically as soon as Kyoko had her contact experiment; within less than a year, chronologically. That means someone knew what was up with Kyoko, and that this makes Asuka a pilot candidate. And that in turn means they probably knew what would happen at her contact experiment and didn't warn her. Instead they were probably glad that this way EVA-02 would get a soul.
