This is my analisis on the three theories:
1)
Eva 00 has no resident soul:If Eva 00 has no soul at all, it means its a 'special' Eva. I mean, Evas 01 & 02 do have souls, so the only one of the 'regulars' without it would be Unit 00.
Then, it would probably mean that Rei has some special ability to pilot it, considering all the things that suggest the relation of the pilots and the resident soul, seems like synchro and resident souls are one thing.
But, if Rei has some special 'kaworu' like powers, then, how could Shinji synch with it (ep. 14)? And what is then that something that invades Shinji on the same ep, the thing that came from inside the Eva, if the Eva was empty (soulless)?
2)
Naoko Akagi is the resident soul of Eva 00:This theory is probably based on what we see on ep 14, a berserker Eva 00 hitting the control room where Rei was standing, and considering the previous relationship between Naoko and Rei 001.
We also know that the dummy plug synchs with the Eva because it imitates the pilots brain pattern and that human soul could not be digitalized, and the fact that not any pilot could synch with any Eva. Each Eva had its dedicated pilot, and we know both pilots mother souls dwelled inside Evas 01 & 02. Thus we can discount that there must be a soul in the entry plug to synch and what synchs with the resident soul is the pilots brain patters. Now we can talk about similar brain patterns, because Rei synchs with Eva 01, and Shinji synched with Eva 00. That was possible, as Ritsuko said, because Shinji and Rei's brain patterns where similars. We know that the body of Yui was used to build Rei. So we can assume that Rei has similar brain patterns to both Yui and Shinji (mother and child), because Rei and Shinji swap evas. So, it would have been impossible for Asuka to synch with another Eva, because she has no close blood-bonds to Shinji, Yui or Rei.
So, after this, how then anyone except Ritsuko could have piloted an Eva whose resident soul is Naoko Akagi?
3)
Rei 001 is Eva 00 resident soulThis is my favourite. Here's why:
When on ep 14, Eva 00 goes berserk, we see this Shinji dialogue:
Shinji: Ah What is this?
Something is enterin directly in my mind. What is it?
Ayanami? Ayanami Rei? Is it Rei?, this feeling....
Ayanami? Isn't it her?
So, Shinji feels something entering his mind, something wich seems Rei, but its not Rei (that las "it isn't her?" even though it looks like an affirmation, in fact is not. The original Japanese said "Ayanami? chigau no ka?", wich sounds more like a 'False' Ayanami, denotes a difference in general. Chigau means "to differ (from)"). So we know that there must have been a soul in Eva 00 because Shinji could synch with it, it could not be Naoko because of the brain patterns, and we know something that seems Rei but isn't Rei tried to enter Shinji's mind. Rei synchs with Yui and Shinji synchs with... Rei, Rei 001, that's the impression to me, for two reasons: first, Rei 002 doesn't seem to be wacked off like Kyouko after the contact experiment (soul imprint on the Eva, same as Yui's accident), and that bizarre image of Rei we see when Shinji loses control of Eva 00, the last image, a warped chibi looking Rei.
Originally posted on: 09-Apr-2003, 08:54 GMT
I'm meant to be the one who posts a response like that 
