My roommate pointed me to a couple of articles about Matrix: Reloaded that tackle the deeper meaning behind what we moviegoers saw in the film. His self-described "wild theory" about what really happened is actually something that I posited the night I saw the film to several witnesses. Only they will know that I SAID IT FIRST. Of course, I didn't say it with such verbosity as Phillip Winn, but then I have a day job.
As with me, Philip won't be sure until he can see the film again. Like any complex movie, Matrix: Reloaded practically demands that you see it twice to absorb it all. He describes his thoughts from second viewing here.
I highly recommend reading these articles after seeing the film -- they are chock full of spoilers. But read them nonetheless.
Update: Here is another excellent article.