Psaiyan Prince Vegeta <ppvegeta@hotmail.communism> wrote in 
news:n780kv8vdnn5d8ems75q8c7cpr2itits71@4ax.com:

> Now, I'm not suggesting that she is necessarily having sex with him,
> but do any of you think that Rei has *some* degree of physical
> attraction/romantic interest towards Gendo at the start of the series?
> 
> She seems to like being around Gendo - only smiling and looking happy
> when talking to him. They spend a lot of time together.
> 
> She is very defensive of Gendo, slapping Shinji for badmouthing him
> (remember, she was completely unconcerned by Shinji inviting himself
> into her apartment, groping her or seeing her naked).
> 
> She keeps Gendo's glasses as a memento and carries them around with
> her everywhere (again, she gets annoyed when Shinji is messing with
> them) - keeping a piece of him close to her heart?
> 
> It seems to me that Rei does have a crush on Commander Ikari (well he
> *was* petty much the only man in her life at that point), though she
> probably doesn't fully understand the true nature of such feelings and
> would never act on them unless Gendo was to make the first move.
> 
> There may also be a small degree of vestigial genetic memory from Yui.
> Perhaps it's just a subtle feeling; a tiny impulse at the back of her
> mind, a faint shadow of the wife and lover she was, compelling Rei to
> become close to Gendo once more...
> 
> I'm not going to go into Gendo's thoughts on Rei here but needless to
> say, I'm sure the thought of getting intimate with her crossed his
> mind at least once when he saw his wife's enhanced clone growing up
> into a beautiful young woman.


Personally I think it's more of a Father/Daughter relationship. Up until 
that point Gendo is really the only person to care and/or show an 
interest in her well being.

There might be some form of attraction or crush but as Ayanami doesn't 
really understand her emotions well I don't think she would know exactly 
what it was.