Mr. Tines wrote:
Shinji was the child of his body, and Rei the child of his making. Asuka was just another NERV staff member - and how often does the CEO speak to a shop floor worker?
This. He pays Misato good bucks to deal with the pilots, & has no reason to interact with her, he's not the sort to just chat with her for the heck of it.
For what it's worth the Manga has a scene where she gives him the "suck up to boss" treatment and tries to invite him for dinner while she & Shini were training at NERV hq, & mocks Shinji for being dejected over his refusal.
I don't really see it as OOC, like he's a person and nor barking out the command voice 24/7 but, it's not like he really engages them.
In canonland she seems to have a fairly diffuse opinion of him, like, he's just part of the unfair world/ impersonal organization that ought to admire her more (at the start)/ doesn't care about her (towards the end), though she does view him as playing favorites (though even that more through the lens of seeing Rei as an obedient suckup/doormat), sort of as a child views a vague authority - Unlike how they always have her clearly know who he is and look down at him in fanfic.
It kinda shows hos disconnected Shinji is from his origins & heritage that no one really gives him the "boss' kid" treatment, no sucking up or deferrence etc. (except perhaps that time Misato remarked that they both have a rather somber demeanor in ep 1, before she knew the situation)
Though Fuyutsuki & Kaji respectively inform him of Yui's involvement in the project in the Manga/Rebuild, he never finds out in the original, nor does he ever find out about her background in SEELE. I suppose it's part of EVA's whole unconventional story structure, like, Shinji never even meets Keel, there's no "final confrontation" with Keel, Gendo or any physical antagonist etc. the closest he comes to meeting the commitee face to face is after ep 17, when Misato decides to get debriefed in his state because she doesn't want him getting interrogated right after his experience with Leliel.
Misato herself finds out about stuff but gets gunned down before she can really do anything.