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.)
Sailor Star Dust: You're correct, 1.0 and its variations didn't include this gag.
Kendrix: 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.
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
Sailor Star Dust: That wouldn't surprise me. Rei was concerned about making sure the Commander's glasses were safe and that Ikari kid wouldn't stop yapping. (It seems she didn't hear him at all, like the later scenes indicated.)
NemZ: Perhaps he was still suffering a bit of thermal expansion? :P
thewayneiac: Of Course! Morning wood, it all makes sense now!