The Shinji in this story is a lot more adjusted than his original counterpoint, a lot more accepting of his flaws, and is able to call bullshit on his old values when even called out upon them.
In the old series, Shinji was so wrapped up with his faults and flaws (being called a "pervert", not having any value outside of Evangelion, making mistakes, or having to be "perfect" so he would have any value in the eyes of others.), that even IF he was perfect, it wouldn't be enough for him to not be paranoid of the people around him and how they would view him. Thankfully, due to the efforts of the Doctor and some healthy psychology, this Shinji now realizes that such views are immensely unhealthy and that it's natural for people to make mistakes. The trick is that you have to be willing to admit you made mistakes and work towards atoning for it, not wallowing in self-pity thinking that nothing you do will make anything better.
Heck, I'm detecting a bit of "Doctor-isms" in Shinji's dialogue, and that just makes me squee with joy seeing how Shinji has improved.
