If I may speculate: its important that this episode is number two of the trilogy. It sounds to me like elementary school buddism; reincarnation and all that. Like a retelling of Sidhartha the hero must keep re-doing life until he comes to realize the ultimate futility of it.
Perhaps the final installment will end w/ Neo gazing out onto the Blvd.(river) from the front window of his favorite noodle shop. He will realize that all that has transpired has taken place in the proverbial twinkling of an eye. If he looks closely out into the street he can see himself, dark glasses, long trench coat, moving stealthily to some grim confrontation w/ Agent Smith.
Just as the profundities in the Old Testament was told in language that a shepard could understand, the "Matrix" is revealed to neo in a language, digitalese, that he can understand--and more importantly, believe.
The story remains the same.