Shinji raises the upper half of his body and the blanket drops up to his waist
Shinji, looks blankly at the plug suit
Rei speaks, coldly
Shinji does not know what she is talking about
REI:“Make sure you don’t accidentally show up like that.”
EvangelionFan: Rei has no reaction to Shinji's bare-nakedness. (If I recall correctly, this little gag is not included in Rebuild 1.0.)
Kendrix: As we see a bit of his upper tigh, it is safe to assume that Rei got the full frontal view. She is as unfazed by seeing naked people than she is by being seen naked herself - She even assumes that Shinji might just causually forget to wear clothes.
Rei doesn't seem to realize that her attitude towards nudity is much different from that of others.
arael: I never really got that line form Rei... "To show up like that"...
Like what? Naked? Gloomy?
Waitaminit... Was that Rei humour?
thewayneiac: I always took it as deliberate sarcasm. Maybe she's a little ticked off over his absurd behavior that morning after all, and that line is a subtle payback.
Additional Commentary
NemZ: Perhaps he was still suffering a bit of thermal expansion? :P
thewayneiac: Of Course! Morning wood, it all makes sense now!