Was that the religiously original part of it?
It must be tough for you to put up with my foolish questions...
The question that niggles me personally is, How do we even know Neo is real? I think we, as the audience, buy readily into the illusion that Neo is real because we want him to be. But the Agents aren't "real" (or are they?). If they Agents aren't real, why do we assume Neo is? The Agents are supposed to be sentient programs but in that respect how do we ever know Neo isn't simply a similar program? (or any of the other characters for that matter?)
At the end of the day, I think the Wachowski Brothers always knew where they wanted to go with these films. It isn't something they just thought up in reponse to the first film (ie- afterwards). The original, quite plainly, left off with the story untold. My only hope is that they don't flub it with the last movie. Judging from people's reaction to this middle film, I'd say the Wachowski Brothers have produced the desired effect (ie people torn and arguing about what the film is about to this point). This is good (provided the last flick is good) because it keeps the anticipation and suspense to the last moment. I don't want to be able to guess how the movie ends now.
I might come back Wednesday night and offer a conjecture but to this point, given that Neo and company might simply be a version of software- I'll keep my powder dry.