Ikari:“No problem. Another spare will be arriving.”
Woman (OFF):“Direct force on standby in its current position until a pseudonym is created.”
thewayneiac: Gee, who can he mean?
Reichu: I'm surprised Fuyutsuki was in the dark about Shinji, considering how chummy he and Gendo are most of the time. Not to mention Fuyutsuki is one of the few characters who really knows what's going on.
MDWigs: I think this is probably just one of those continuity gaffs. Fuyutsuki should have known that Shinji would be the eventual pilot (since he knows who is in EVA-01), but they needed someone to ask the question.
Hexon.Arq: Maybe Gendo just forgot to inform Fuyutsuki that the kid would be arriving that very day.
OMF: Or perhaps Shinji is simply NOT a topic for discussion with Gendo.
Kendrix: That Fuyutsuki didn't know yet goes well with my theory that calling Shinji was a last-moment ultima ratio type of decision. He turns away from Fuyutsuki before the latter can guess who it is... and so, he becomes opaque to the audience, we can't see his face, so we can't guess what he's thinking. As for what Gendo himself was thinking here, he probably doesn't want to talk about it/would prefer if Fuyu wouldn't confront him about it/ask further questions.