>>2414346I think he might have ended up loving her a a daughter but never stopped seeing her as an extension of his wife either.
As for her, it might have been a purely binary matter, without giving much thought about what kind of relationship they have:
'People I like: Gendo'
'Background noise: Everyone else'
It's not like she had much of a frame of reference to the different kinds of interpersonal relationships there are, until Shinji came into the picture.
