>>2246236I agree, but for Rei III I think it's the negative emotions towards Gendo that won out in the end.
After all, Gendo is the Commander of NERV, the organization that has been keeping her in a lab her whole life, and made it clear that she's replacable.
Rei laments her lack of freedom in a very pessimistic and depressive way when she says that Gendo won't "let her die". She isn't allowed to return to nothingness.
Earlier in the series, Rei insists that she's not the favorite (of Gendo) as Asuka suggests. For Rei, Gendo is both someone bad as her captor, and someone good as the man who seriously hurt himself trying to see if she was all right.
That's where stockholm syndromes come from folks!