Shinji speaks awkwardly, as this is an expression he has rarely used.
Incisivis: Awww…lookit dat. I'd hate to be lumped in with the goofy and coddling breed of Shinji fangirl, but sometimes Shinji just has a kind of sad-puppy cuteness in the early episodes.
OMF: His awkwardness and blushing really gets across how totally unused Shinji is to Misato's genial nature. Judging from this cut, though, he seems to be actually glad he came in. The greeting is his way of making up for his reclusive behaviour.