Shin-seiki: I always thought her face looked especially cartoony in this cut, but I nonetheless consider it very effective the way she frowns when Shinji says "pardon the intrusion". In NGE, moreso than most anime, it is worthwhile to carefully read the expressions on the characters' faces, as Anno and co. have done a very good job of "directing" the "performances" of their characters, with regard to the animation, as well as the voice acting (which I rate among the all-time best in anime).
OMF: Shinji hasn't been responsive to Misato's attempts to start a conversation. One wonders if she's been trying all the way home in the car!
Misato's so informal about inviting Shinji into her home. Shinji's apprehension might have to do with his hesitation to let go of formalities; he has a habit of hiding behind decorum. She's clearly unhappy with the distance he's maintaining.