Yes, you are entirely correct. But between standard-test-pilot Asuka (who, ironically, pilots the production model Eva rather than the prototype, go figure) and tablua-rasa-Rei there is quite a lot of middle ground where an 'everyman' character could sit, and I think Shinji's much too close to the Rei side of the spectrum for the cast to be effective--having two passive and one active character really doesn't work out that well for a proper three-person cast.

Were I in the fanfic writing business and rewriting Eva, I'd probably end up molding it with Shinji expressing more bravado to cover up his insecurities in the situation (kind of like overt-Asuka with covert-Rei, say), and with better manipulation by Gendo to mold his responses into being Gendo's proxy for the situation.

As a side note, I only became aware of the remake of Eva very recently, and was puzzled when I went to check something Eva-related and saw some chick with glasses in a plug-suit. If you're neurally synchronized with your giant robot, why would you need glasses?

>Gosh, this got grim quickly. Let's think about puppies instead.

Well, yeah. It's EVA. It's inherently grim.