I also think it's fascinating (and more than a cooincidence) that Larry and Andy wrote a story which parallels to so many other story universes.
-SPOILER-
For instance: You can link the new movie "The Forgotten" with the Matrix universe PERFECTLY (perhapes one of the earlier versions of the Matrix). You could view the plot from the point of view where the system's running some new program to improve overal control program so subsequently this woman's child is abducted and the system starts making the accomedating changes to the matrix in order to make her think she's going crazy-perhaps to anyalize and obtain a clean breakdown of the human psyche. She fails to follow along with the program and begins to pose more and more of a threat to the system so the system sends an "agent" after her to tie up the loose ends. Nevermind all the speculation about the agent being an alien. They never actually say THEY are extraterrestrials.
Or course, the system's program fails at the end of the movie when Julianne Moore's character refuses to accept the program no matter what and consequently the main agent (obsolete program) is deleted. Then the system resets the matrix just as it was before the failed program was launched.
There's quite a few movies that actually fit in this way. I think it's really fun to watch different moves and see how well it fits into the matrix. You might be surprised by what you find ;-)
there are many sci-fi etc movies that could fit in some way...for instance, I, robot in that the robots have become sentient to the point that they fight back, Dune in that the Machines became sentient, took over many worlds and enslaved them, then (and i haven't read the new book, yet, so not exactly sure how that ends...) machines are overcome, Termintor with the whole humans fighting machines, etc, etc, etc...sentient machines taking over the world(s) is a very common theme in modern and some not so modern writings and movies. It is definitely not a coincidence, it is a logical extension of technology today with history.