Side of Misato's face UP. She accepts his words with an open heart. With a kind, smiling face, here she again returns two words.
Misato:“…Welcome home.”
OMF: Such a touching little exchange. I may weep openly.
Incisivis: The reunion with Misato suggests a rebirth of sorts, being that Shinji and Misato repeat the same greetings as when he first entered her apartment. But there is also a darker suggestion: that Shinji can't escape even when he wants to. It is the right thing to do in this circumstance, but the notion still remains, and it will be revisited in episode #19.
Gundampilotspaz: But when he says it here, he does so with conviction, unlike in episode #02. I think it implies that he really has begun to form emotional bonds with Misato, Kensuke, and Toji, and, also, that he more genuinely regards Tokyo-3 as "home". Before, it was mostly just a place to live, but now he begins to feel as though he belongs. Such powerful emotion backing those two little words. In my opinion, this exemplifies the true power of the first four episodes: the way that Shinji is built up from an emotional wreck to the rather changed person we meet in the next episode.
