I liked how Shinji saw Gendo with Rei, it's got to hurt to see your father turn away from you like that. That never exactly happened with me, but I also can't say I'm particularly close with my dad either.
The scene with Misaton and Shinji as they watched Tokyo-3 rise up was great. These two character's relationship has always been one of my favorite parts of the anime, this scene seems to indicate that that will also be so in the manga. He is grateful, I'm sure, for her words. But, it hurts that it wasn't his father who he heard it from. Validation and support from your parents is something every person; Man, Woman, Boy, Girl, Transgender, whatever wants on at least some level, I think.
Also, the look Rei gives Shinji in the hospital has always unnerved me for some reason.
Really good first volume.It handled the excellent first two episodes really well, I think.