There is one idea from the depths of the old thread that still ghosts around in my head once in a while, I think someone floated the idea of "Something that starts of like ep 26 AU or SRIP verse but gradually turns into something more like canon", Rei starting out AU-like & gradually becoming more like canon Rei etc.
Since then I'd kept thinking of it every once in a while.
There's at least one spinoff Manga - it eludes me which - has Misato move in to babysit Shinji because Gendo & yui are too busy at the lab; Something like that could happen. I mean even "they are from ep 26" and "they are alive & present but are still workaholics" is a different gradation of Happy-AU-Ness.
& the actual SIRP game has this actually kinda fascinating mechanic of shifting between three tones (if you go back from "highschool AU" to the middle route, it looks like Gendo gets a redemption because Teacher!Misato chewed him out in the parent teacher meeting...)
If i ever did that I'd have to restrict myself to "No more than number of episodes +1 chapters per act" and maybe a few extra chapters for setup ( since I've learned from experience that having too many open ended long projects going at once means none gets finished) & if I added any extracanonical chars they'd have to be ordinary classmates.
What might the emotional crux be? You could play it for your basic "I thought the world was simple when I was young but it's complicated" or do something like middle earth's fading in reserve. Instead of the great & epic mournfully leaving behind the mundane, it could be an alienating, confusing "weirdening" of the world (I think that's the main factor keeps attracting me to the idea.)
Other things that are interesting are the possibility of having Gendo & yui be proper parents while still being Gendo and Yui: a ruthless pragmatist & a detached visionary.
That, and end of TV had this whole emphasis on how for the three main children, being an EVA pilot had practically eaten their identities. In the case of canon that was precisely because of how little else their sucky, trauma-filled lives contained for them to derive self-worth; The AU sequence is a wakeup call like, "Hey look there's parts of you unrelated to piloting"
An ambitious fun way to add structure could be to switch one gradation of "normal AU"-ness per storyarc.
At the end you would have the same result of "people possessed by EVA" (in the sense that Misato uses that phrase at the end of ep 23), and what they were at the start would seem like a faded dream - The mood would be something like this song
, or perhaps this one
At least, at the time that the story reaches its "belly of the whale" moment. The ultimate conclusion would probably emerge along the way.
And what would be the logical end point? Something EoTV-like? (maximum weird... like serial experiments Lain) Maximum dark (Q? Something like Devilman Crybaby?) or just "EoE with minor differences"? You'd have to dynamically follow it where it goes I guess...
Edit: Found it! Look how old it is: post/817403/From-Your-Lips-to-the-Authors-Ears-Story-Ideas/#817403
I'd say that it would require at least some pre-sachiel prep time to make it feel like Gendo & Yui are there before they disappear. Maybe they do SIRP-esque random activities meant to be training. Or you'd have some time when Shinji & friends do fun stuff in the foreground while not yet knowing much about what their parents are up to but Gendo & Yui are already busy preparing behind the scenes.
Maybe the story begins when Rei transfers like in ep 26 but it's the equivalent of Rei joining Touji's & Kensuke's class one year before.
Or there's a prologue where they're happy childhood friends but when they meet they're different, because trauma (or, in Rei's case, because the one they knew was Rei I; in any case Gendo & Yui introduce her as "distant cousin" but they most definitely cooked her up in a test tube )
Alas poor Kaworu, I knew him well...