Spoilers in response to web:
as for smith, he was copied into the body of the zion native, right before he picked up the phone to exit the matrix, thus sending him into the actual body of the guy. At the end of the movie, they are talking about how the defenses were screwd up because someone used their energy blast too early, well if you play the matrix video game you see that the copied smith was the guy who sabatoged the defenses, and then lives to go after neo.
as for the oracle, i believe she was created by the matrix, to hold control over the one even though he has made his enlightenment out of the matrix, if he believes she is telling the truth, the matrix could make the one do whatever it wants. just as the key maker was created to allow neo entrance to the source, and cause the destruction/rebuilding of the matrix, the oracle was created to instill the belief that what he was doing was for the good of all.
oh, and with the zion rave/sex scene, im betting that in the next movie we see a niobe/morpheus doggy style to anal full penetration, while they listen to dave ralph.