"Hey, what if Neo, or at least part of him, was killed when the bomb went off? This is how he is picked up by Mero. However, Neos will did not allow him to die, because he cared so much for Trin, that he could not let her die. So his mind got out, while still being in the Matrix. "
yes yes, I would go along with the seperation thing. think back to the first matrix...the pivotal point in the movie, when he dies!! perhaps thats when we first notice he was seperated from both matrix's (real world and reg matrix). And then he mentally ported back in when trinity told him her feelings.
I can see that happenening.