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.
Sephizim: It seems to me that this is the moment that marks the beginning of Shinji's shift into being less able to be open with Misato. Funny that it happens after she brings up something they actually have in common. When she was a nebulous unknown entity, she was approachable. Now that he know something about her, suddenly he doesn't know what to do.
