So I read up on the Wikipedia article about Thrice Upon a Time and found this at the end:
That very day, in this third iteration of the timeline, Murdoch and Lee go out shopping in Kingussie, and a certain young woman named Anne trips over Sir Charles's kitten... This is the origin of the story's title, Thrice Upon A Time.
Why I think that's relevant here:
If Shinji goes to Wille's home base in Shin, this will be the third
repetition of Shinji coming to a new home. 1.0:
Misato brings Shinji to Tokyo-III per usual. This sequence ends in failure in 2.0 with Eva-01's awakening, the destruction of Tokyo-III, Rei "dying" and Shinji peacing out for 14 years.3.0:
Shinji's arrival at Wunder and flight Neo-Nerv HQ mirror the events in 1.0, but turned on their head in a dark reprise where everything's all wrong. Once again ends in failure when Eva-13 upends everything and Kaworu "dies". Asuka's not letting him peace out again though.3.0+1.0:
Asuka drags Shinji back to the Wunder again, and...
Will he get it right this time?
Someday I hope that we'll be reunited if that is what's destined to be. Perhaps we'll discover that elusive bible. And then we will finally be free!