Possible spoilers for EVA. You have been warned.
However, I don't see Rei suddenly acting like a completely normal
teenage girl. I also don't see her pining after Shinji like that--
remember, she is more of a mother figure than a romantic one for Shinji. I
do have to agree, this change seems far too extreme. And I must also agree
that it seems the author hasn't seen very much, if any, of Evangelion.
<Possible Spoilers.......>
In one of the last 2 episodes of the series, Shinji imagines a
reality where everyone is "normal". That is the *only* possible
tie in I could see with this fic... Perhaps an explanation from the
author would be advisable?
-Anand