Serious question. They know he's naive, overly emotional and can unleash another apocalypse. So why does the captain bring him back/cone him???
Tucker's Law: http://www.youtube.com/watch?v=xe3Ou9xBAlI
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He's the only one that could possibly pilot Unit-01 which Nerv needs to complete the Human Instrumentality Project. Misato and WILLE don't want that happening so they kept him under wraps. Shinji wasn't brought back he simply was awakened after the fight at the beginning of the movie. I also think that this isn't really Shinji but a copy/clone but I could be proven wrong.
I will not fear, fear is the mind killer