A naked Shinji's attention is caught by Misato's hanging undergarments.
thewayneiac: Ugh, did they have to show us that?
Sharp-kun: I pity Pen² in this shot.
Reichu: Non-humans are blissfully indifferent when it comes to matters of sex. I doubt it makes any difference at all to Pen² whether his roomies are nude or not. (It never did to the conure I used to shower with.)
tv33: And they say anime girls are too thin. They must not have been feeding him at his former teacher's home.
Reichu: Well, many adolescent boys have the bad habit of being ridiculously thin regardless of how much food you put into them.
Hexon.Arq: It's probably for comical effect that he is so thin. If he were as well-developed as he appears later on, this scene wouldn't be as funny. There'd be more hooting than laughing… none from me, of course.