Great movie, eh? It's one of my favorites.
The 2nd and 3rd aren't as good but I still like them a lot and enjoy the ride.
I know that the Wachowski's are comic book fans and before those movies were made there was a comic book trend that, "everything you know is wrong."
If you want, check out Grant Morrisson's The Invisibles. Grant was even pissed off that some of The Matrix seemed to be a blatent swipe of his book.