This is my first post here so im sorry if im posting stuff thats
already been talked about, i just wathed death : rebirth and end of
evangelion yesterday and have some thoughts i want to share:

I was reading the FAQ at http://faq.pen3.cjb.net/ and saw that the
answer the whos soul is in Unit 00 is unknown. Isn't it possible that
the soul is the one of Naoko Akagi? Whenever Unit 00 go berserk it is
targeting Rei or Commander Ikari which would suggest that.

Since Unit 01 and unit 02 has their respective pilots mothers souls in
them i think we can assume that this was the plan for all EVA:s. It is
also known that all students in Shinjis class at school are potential
EVA pilots. I think that all the students mothers have worked inside
NERV and this is the reason NERV has access to their souls and all the
children has been put in the same class. Makes sense if you take into
account that they are some of the few remaining people in Tokyo-3
which could have to do with their parents beeing NERV employees?