Damn, that scene with Shinji was like a punch in the gut for me. "You didn't want me. You can't have me now. You can't come back for me now." The entire scene was powerful, actually. I think the image of Gendo lying in a pool of blood and the Eva speak for themselves. I can't help but feel there is some sort of animosity that Shinji feels for his mother as well.
Asuka is worried over Shinji, it seems that the manga continues to hit at her feelings for him just a little more overtly than in the anime. I'm cool with that, of course. Between Kaji's moment with her and Misato it feels like he knows his time is just about up. I think the women felt something odd about him as well.