Once 4.0 comes out and gives us a satisfying conclusion
Yeah. Like that's gonna happen. Anno is all about unanswered questions and coming to your own conclusions. Closure and satisfaction are the furthest thing from his mind. He's going to leave Shinji and the audience disappointment. and the message is ultimately going to be about learning to live with it.
So if he was destined to fail and endure eternal suffering, then the others should join him in it.
Anno wont do it. But for me personally, I would just have Shinji become a bad guy. The entire universe is conspiring against him. His friends and family have abandoned and mistreated him at every turn, or are dead/have outgrown him. He's never going to be able to go back to having a normal life ever again after this.
It would be immensely Catharic for me if he just gave up even the pretense of trying to be a good human being and just embraced his dark side and became an Irredeemable Supervillain just as bad/worse than his father. If he's never going to be redeemed and will have to spend the rest of his life apologizing for something that wasn't his fault anyway, if theres no hope for him being forgiven, if the world as Eva really is that cruel. Then he should just give up.
Yes it would be a terrible message to send. It's the only one that would be in any way emotionally or intellectually honest. It would be great to end the series on a tragic and grimdark note. The world has basically put him in a position where him being a monster is the only way he'll ever be allowed any sort of autonomy or control over his own destiny ever again. He can either spend the rest of his life miserable, or he can hurt the world back. Either by directly lashing out against it, or more in character for Shinji. In a passive Aggressive way.
I imagine a scene like in EOE after the hospital room scene. Where they need him to pilot again, and he outright refuses. Just to spite the world who ruined his life.
"Why should I help you Misato? It's already my fault."