Jason's contention (correct me if I'm wrong) is that while the first movie did in fact explore some deep philosophical issues, the second and third movies only had the appearance of depth without the actual substance.
I refered to this site where there are several philosophical essays which the Wachowski brothers released alongside the second and third movies. I feel that this is the best evidence that I can show that they considered more than just the surface of the philosophy that appeared in their movies. Other than that all I can offer is my opinion, for what that is worth.
I think that the Matrix trilogy moves us from grey to black-and-white to a multi-colored world. The grey is the meaningless fog in which Neo lived as a software developer. Then Morpheus and the gang (jinkies) led him on a journey of discovery where he saw that there is a conflict going on that is much greater than what he had known. Finally, Neo continues on this journey to learn that in this battle there is not a clear distinction between good and evil due to "race" or "religion" as there are evil humans and good machines. The world is full of color, the fog has been lifted and the details are becoming more clear. Smith wants to keep the world in the grey/black area, thus they must fight.
What do you think? Good or lame?