Lilith endowed Shinji with a spine by bringing Bright Noa and Kouji Kabuto from their respective universes between scenesNoa slapped Shinji -a tactic whose efficacy has been scientifically proven many times - and gave him a long lecture about duty and responsibility, and Kouji talked him about the importance of never giving up, fighting to prevent other people of getting also hurt... and explained to him how dealing with Tsunderes.
There will be a Crossover featuring the Shinjis, Asukas and Reis of Nobody Dies, The Second Try, Once More with Feeling, RE-TAKE, Shinji And Warhammer 40 K, Thousand Shinji, Children of an Elder God and Evangelion 303At some point of the crossover they will travel to the original and Rebuild universes. Butts will get much ass-kicking, Gendo, Seele and even Yui will get a reckoning, each Canon Shinji will get his red-haired girl and each Canon Asuka will get her not-so-wimpy-now Shinji.
A certain picture of Gendo will be made publicAfter which he'll lose everything, as nobody will ever take him seriously again.
The Fourth Child will be KensukeToji has no incentive to pilot this time, because his sister didn't get horribly injured. So, who will be Fourth Child? Kensuke, for several reasons. He's a military otaku, so doing this would be a dream come true. Being a pilot would seriously improve his status at school. From his perspective, it might help make up for needlessly risking his life getting footage of the Fourth Angel. And it would help him get closer to Rei.
Alternately, the Fourth Child will be ChihiroPossibly as part of a desperate scheme to have Shinji as her boy-toy.
Shinji has part of his mother's mind/personality as a result of InstrumentalityHe's frequently compared to his mother in terms of personality, so the changes might be the result of a kind of mental fusion.