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HeWhoPostsStuff: Shinji seems surprised after he hears Misato say this. Perhaps he thinks that all people who have a bad relationship with their parents end up depressed and antisocial like him. I think he's caught off guard by Misato's revelation about her father, since he's seen her so cheerful up to this point, maybe it makes him reconsider his own actions for a moment…
Hexon.Arq: I always interpreted his reaction as being a sort of a slight recoil to the possibility that she's either going to start talking about herself or expect him to do the same. Presenting commonalities with such cryptic remarks is usually done for this reason. He's probably just waiting for her to continue speaking, or he's suddenly uncomfortable at the prospect that she'll try to subtly dig into him.
