Shinji:“Ugh!! I didn't come all this way for something like this… This is all wrong!”
Shin-seiki: This darkening over of the eyes (also seen in C-252) is a common anime visual convention, used to indicate a character's mortification or otherwise being totally bummed out. (Another occasion that comes to mind, where it is used in NGE to depict someone's acute mortification, is this.)
Sephizim: Breaking point. He obviously has some affinity for Misato, and seeing that she's now angry at him (or at least that's likely how he perceives that line), he pretty much wants to crawl in a corner and die. He wants nothing more to be away from this situation where people are angry at him, his father is as much of a douche as ever, and they're trying to get him to do things he doesn't want to.
