@Lunaryon If I could have your feedback, a couple of potential questions for Shinji to ask.
[_] "I've talked a lot to both my psychiatrist and gender specialist about us. I think I know the answer, to this question, but just to hear it in your words: In the 6 years you raised me, have I done, or not done,
anything to make you loathe me so; and if I have what restoration can I do make up for six-year-old-me's tresspass?
[_] "I remember being hungry. People in dark clothes came and spoke to you and then you stayed in your office for 3 days nonstop. I remember knocking on the door saying I was hungry. I remember your face when you opened the door. If I ever did forget it, my nightmares would remind me. Not a hour later I was on a train against my will, bound for Uncle. My question to you is the same one she asked as the train doors closed. "Why father, why? Don't you love me?"
[manga reference, after the 13th Angel's attack] I don't see any sharp knives around this time. Smart. (After the 13th, towards the end of Shinji conversation\falling out with Gendo, Shinji tells Gendo "I -told- you: don't leave me alone with you and a knife!".
I realize that Sakamoto, not Anno wrote the manga, but that line stuck with me. It was something anime Shinji would never say. There is a lot of history packed into that line, and that's fascinating. (Manga Shinji always had a subtle undercurrent of soldering anger. It made Shinji seem more like an actual moody teenager most of the time.)