If Shinji was female instead of a male (in that case he would have
been named Rei), would Gendo have still been the neglectful parent?
One could say one of Gendo's reasons for alienating Shinji was because
he saw the boy as a version of himself (which he probably loathed).
However, a Ms. Shinji would look more like Yui, and that might cause
Gendo to be more affectionate to his offspring (even thought he would
still be manipulative). Gendo did hang around with Rei I a lot after
all (sharing with her some unappealing comments about a certain
lover/co-worker, with fatal consequences), and it was not entirely
because she was useful to his Instrumentality plans.
BTW, did anyone in the cast who did not know about Rei's true identity
(Misato, Asuka, the schoolkids) ever notice that she shared a strong
resemblance to Shinji?

A.Gerard