the journey of Neo and his rejection, possible failure, and the complete impossibility of him being a messiah in any religious or spiritual sense of the word. She might not be there to help him. This is a scene that puts humanitys true nature diametrically opposed to everything the Matrix represents. Whether or not one believes Neo was a Jesus-figure, itd be hard to argue that it was a role that Neo at all embraced.
It was meant as a form of control to keep you in line. What an easy choice for a messiah. As he says, I just wish I knew what I was supposed. It is true, the first film portrayed him as a messianic figure, at least in theme if not word. As an atheist who has religion pushed down my throat daily in this country it was personally vastly annoying to me that people took such an anti-religious, anti-dogma film and tried to turn it into a generic retelling of Jesus resurrection and sacrifice. Zion, the people who need to believe in something, and the movie-going public are the ones who thrust that upon him. Again, its Morpheus role to embrace him as the Saviour. Might be ok, let's wait and see. There are four gospels in the Bible; that of Mathew, John, Luke and Mark. At that point anyone who tries to hold onto a Neo is Jesus or any sort of messiah ideal is just deluding themselves. Neo, led by Morpheus prophecy, continues down the path of the One. Beyond that there are four aspects of self; the mental, physical, spiritual and the natural.