Spoilers below. Don't scan this unless you've seen the movie, and aren't quite sure what's going on. I'm going to break it down as I seem to understand it.
The storyline about there having been more than one Matrix was established as far back as the first movie. Agent Smith was discussing the previous "versions" of the Matrix with Morpheus when he was trying to get the codes to the Zion mainframe. It was also foreshadowed (or telegraphed, if you prefer) several times in Reloaded, such as the french guy talking about Neo's "predecessors".
The first Matrix was perfect, but no one would accept it. With the help of the Oracle, they created a flawed world that gave people "choice". The problem is that while more people than ever accepted the falsity of the world, by definition, a small contingent would NOT accept it. These people would break free and rebel, freeing others, breaking down the system. In order to fix this "problem", they created a Messiah, "The One", Neo ... who would actually bring about the destruction of the ones who were freed because they believed in him. However, again, the problem of choice is handled, but it's not a "real choice. The One is given the choice of picking a few people to rebuild Zion with, or going back to the Matrix to save the ones he loves, in this case, Trinity. Predictably, Neo chooses to go back, fulfilling his "purpose".
There have NOT been six different versions of "The Matrix". There have simply been six different ZIONS, each time destroyed by the machines, unknowingly betrayed (even unbeknownst to him) by The One. Zion is an eventuality, the result of choice, although just as predictable a result as anything else. The One is a trojan horse, sent to infiltrate Zion and bring about it's destruction ... and that's why Neo can do the tings he can do. It's his purpose.
That's right. Neo is not real. He's a program with a purpose, just like all the others. I'm under the impression that "Revolutions" will deal with Neo taking a path that was not predicted, using the flaw of choice to choose to fight his own purpose and destiny and try to end the cycle. I'm still not entirely sure what the reasoning is behind Neo being able to use his abilities outside the Matrix proper, but I'm working out the logic behind it. Perhaps Neo is simply a machine himself?