Yeah, who said she was one? She seemed like a capable commander to me.
With that being said, I've been doing some thinking ever since I got my copy of the movie and I found something in the viewings that made me think that things are a lot more complicated than it appears regarding Shinji (I watched it again a couple of nights ago to make sure I wasn't mistaken on certain points). In order to tell you what conclusion I made, I want to go through some plot points from when Shinji is on the Wunder and show how I came to my conclusion:
1. As he is being wheeled to the Wunder's bridge, Shinji is under heavy restraint, with four guards aiming automatic rifles at him. For someone of Shinji's size and stature, this seems pretty excessive. I don't have a lot of upper body strength compared to other guys my age, but I'm sure I can backhand the kid into next week if I had the inclination. I also remember reading somewhere on this forum (I think Bagheera was the one who wrote it) that law enforcement and security personnel are trained to only aim their weapon at someone only if they know they're going to shoot. One would think that moderate restraints and one guard with a holstered pistol would be enough. The film's events only show that he is a danger when he is in an Eva, so what would warrant such security measures?
2. Again as he is on the gurney during the transfer, we get a shot of his feet. On Shinji's right foot is written in what appears to be black marker "BM-03" while his left has "S.Ikari?" written. Now, it's obvious that they were unsure if it was really Shinji. But we can also see that if there was a BM-03, common sense dictates that there must be a BM-01 & BM-02.
3. When Misato asks Ritsuko if it is Shinji they have in front of him, She replies that he "seems to be."** Even though she says in the next sentence that his physiological and dental patterns match those made before N3I, Ritsuko chooses to remain vague on her part. Later when Shinji was transferred to the quarantine section, he was still referred to as BM-03 and that they're calling him his given name on a provisional basis. If his records were a complete match between then and now, why is there still ambiguity over whether or not it's really him?
4. After the Mark 09 takes Shinji and they fly off, Asuka remarks as she sees the jet trail, "This Shinji is not only an idiot, he's a brat." (Italics place for empathasis)
So what conclusions can be drawn from these four items:
1. During the timeskip, there were at least two beings with Shinji's image and likeness, even down to sharing the same DNA pattern.
2. These beings had unique abilites such as enhanced strength or speed.
3.They are very dangerous and to let your guard down around them is to put your life in great peril.
If this is the case, it would explain the cold reception Shinji got on the Wunder's bridge. I mean, would a person be smiles and sunshine if you think that kid might try to kill you? So if the cast has bad memories of Shinji, it might not be of the Shinji that we see in the movies.
**Of course, I'm using the Home release subtitles as they are the offical English translation of the film. I understand that there are fan-produced translations that might say something different, and as I've read that translating Japanese to English is more on an art than a science, it's understandable that the accuracy or inaccuracy of the lines I used as evidence might be subject to scrutiny and debate.
That's pretty much it. This is the first time I've delved into something this much regarding Eva. I have more to say regarding this subject, but it would be specualtion and this thread might not be the right place for it. I should also note that jcmoorehead's post-3.33 fic, "Hand Cannot Erase," touches the subject a little, so I was convinced I haven't completely gone mad. If any mod or admin feels thsi should go somewhere else, feel free to move it. Thank you for your time.