Then the oracle says that the choice has already been made whether or not Neo is going to let Trinity die. He only needs to understand why.
Finally, at the end, The oracle notes that she is now a believer that he is the one, whereas previousely she was not.
In the last movie, the oracle said he was not the one, noting implicitly that Neo did not lead the "examined life" (know thyself)."
At the time the Oracle talks with Neo and tells him he's not the one, he is not yet in love with Trinity. She tells him that "being the one is like being in love" or something like that.
IMHO, That is the difference between him and the other 6 and the reason he isn't a program.
Or... maybe it's the reason he is such a special program, because he's an AI that learned to love in the same way that his counterpart, Agent Smith, is learning to hate.
Just grasping at straws here...