Check out this really in-depth analysis of The Matrix Reloaded.
My basic thesis is that Matrix Reloaded is a story about Genesis. Not the creation story. I mean the transcendence story that comes immediately after the creation story, in which the serpent, who is Loki the Inventor God, who is Neo, leads humanity from the Garden into Middle Earth. (I have a sneaking suspicion the three-movie arc is going to be about machine evolution as well.)