Another really good observation I’m plucking from evageeks is that angel cores act as gateways to the Anti-Universe; that plug depth can be dangerous because it puts the pilot at risk of disappearing into the Anti-Universe completely, and Yui’s disappearance during the early days of Eva development was an example of this exact phenomenon, explaining Gendo’s comments in 3+1 that he travelled to the A-U in search of her. And it follows, then, as this poster points out, that Shinji’s strange absence between 2.0 and 3.0 would be another disappearance into the Anti-Universe.
It’s particularly interesting that Wille operatives in 3.0 consistently refer to Shinji as a copy of the original generated within Unit-01, rather than the same Shinji retrieved from 14 years of stasis. Even inorganic objects, like his father’s tape player, have been “restored”, rather than just recovered. Which makes sense; Instrumentality is the process of breaking everything down and building it back up again, and the Anti-Universe seems to be the stage on which Instrumentality takes place.
But it also seems worthy of note that this process of dissolving into LCL then being born again from LCL as a perfect copy at the exact same age is exactly the process the Ayanami and Shikinami series of clones go through. Which has to cause one to wonder; is the so-called “Curse of the Eva” that causes pilots to stay forever children actually just a symptom of being constantly dissolved and reformed at the age of 14 every time they enter and exit the core of their Eva?
And if the Anti-Universe doubles as the gateway to a higher plane of “reality” above the plane of “fiction”, then could it be that every time the souls of the pilots are “projected” back down into their flesh bodies at the age of 14, it’s because their “true” “real” selves are 14 years old? Or perhaps more likely, since this physical immaturity seems to represent mental immaturity that must be overcome, the “Curse” is such that so long as the pilots continue to be reincarnated over and over in the world of flesh, they will never grow; and the only way for them to finally move past 14 years of age is to emerge into the “real” world, a world without Evangelion, just as they all do at the very end?
thinking back on this as I do some reading. it feels pertinent to point out that the “Guf” referred to by the “Doors of Guf” that lead into the Anti-Universe is, in Kabbalistic tradition, the chamber wherein unborn souls reside; in essence, it’s a womb, and indeed the “Doors to Guf” in the original Neon Genesis Evangelion appear as vaginas:

and though the New Theatrical Version seems to have for the most part dispensed with the idea that the Eva represents the pilot’s mother, it is still explicitly true that Unit-01 is Shinji’s mother Yui. it makes perfect sense for Unit-01’s entry plug to take Shinji to the very same cosmic womb that the Doors of Guf lead toward, and for him to be literally re-born every time he emerges again.
though it may have been implicit the first time around, I think it bears emphasis that the “Curse of Eva” is in fact a microcosmic version of the problem faced by the whole Evangelion universe; “so long as you continue to pilot the Eva you will continue to be born again and again into the same fourteen year old body” is merely a synonym for “so long as Eva exists everyone in the world will continue to be born again and again into the same sequence of events”.
this could be even more literally true than at first glance, too… since the cosmic mother of all reality is an Eva herself, Evangelion Imaginary, the universe of Evangelion could in fact be in the process being born again and again from the womb of an Eva? it’s certainly relevant that 14 years is consistently the length of time between each Impact that causes the rebirth of humanity; the whole world, just like the pilots, is being reborn at 14 years of age every time, ad infinitum…