Matrix fans,
I remember an interview where the Ws said that the matrix movies are about evolution. Evolution of what? The evolution of man and the way (s)he thinks. Now, Chadwick could have spent all day figuring out new ways of showing you this. If I used the "Chad is an idiot" thread as a benchmark, few would have spent the time to figure out. Instead, he went for the logical (familiar) choice: an X-men spin. Of course, all us comic book fans know that the X-men represent the next step in mankind. In other words, evolution.
The background is as such: after Neo setup the system where the two warring factions work together, freed-man was allowed to evolve on its own. This evolution lead to...the rest is Chadwick's supposition, i.e. the Matrix Online storyline.
And, keep in mind, no matter what medium it's under it is still a comic book.