> My take:
>
> Door #1: We'll be rebooting the Matrix using information we'll be getting from Neo to make it better than before. With this data, we'll be able to plug all the security holes Neo has been abusing - all those loopholes in gravity, laws of inertia, and time perception. Neo can bring along several of his friends who will retain their personalities in the new Matrix.
>
> Door #2: You can go back and try to stop it, but we'll still be rebooting the Matrix, which means erasing and rewriting all the human's memories plugged into the Matrix. This time, Morpheus will be a shipping clerk. By choosing this door, we won't be able to fully analyze Neo's data -- the clues that allowed him to realize what the Matrix is and how to manipulate it. We'll try to patch the security holes in the new Matrix, but we probably won't get them all.

I have a very different understanding of what's going on. A lot of people seem to be saying that the One/Anomaly is something the Architect purposely designed. Rather, I think it is a bug in the system that the Architect (or "his" collaborator -- still not sure if this is the Oracle or not) has controlled for. If the Architect could be rid of the Anomaly, he would be, but as it is the Anomaly is the personification of a design flaw, and the best the machines can do is to keep redesigning the Matrix and incorporating what they learn from each iteration into the next.

With this in mind, here's what I think happens with each door:

Door 1: This is obviously what the machines want, and why they created all the trials and whatnot for the One to undergo -- this is their attempt to control for the Anomaly. In this scenario, Neo surrenders to them and they scan his brain or whatever and are able to resolve their mathematical flaw, creating a new Matrix that has adjusted for his "anomalousness." Zion (and its inhabitants) get destroyed, but Neo gets to survive and pluck 20-some people from the Matrix to form the new Zion. After several generations, another Anomaly will emerge in the system, and the machines will repeat the cycle.

The reason the machines continue to undergo this process is because 1) they can't stop the Anomaly from ocurring and 2) since they can't stop a small percentage of humans from escaping, they need to keep the number of free humans at a manageable level. The Architect says this has happened about five times (the current Matrix is version six, but since we know the first version was radically different than the more recent incarnations, there may not have been an Anomaly that emerged). What we know from the previous movie suggests this: Morpheus refers to the person who first escaped, who had similar powers to Neo. Presumably, this was Neo's predecessor who didn't really escape and founded Zion so much as he made the bargain with the machines.

Door 2: Neo tells the machines to bugger off and does his own thing. The machines are still going to destroy Zion, but since they don't get to scan his brain, they can't correct the bug in the Matrix, which causes it to crash. This kills everyone in the Matrix, and since the machines are about to destroy Zion, it means the end of the human race. Neo choose this, and now has about 24 hours to figure out a way to 1) Stop the machines from destroying Zion and 2) either free the humans from the Matrix or stop it from crashing. I expect the "Revolutions" referred to in the title of the third movie are humans being freed from the Matrix.

Stephen