My sister suggested that the ones who'd probably understand that conversation the most would be programmers, since all his talk of anamolies and mathematical properties regarding both Neo's and the Matrix's creation are very similar to the workings of programs today.
As I understand it, like Makg said, there were 5 other Neos and Zion "incidents" previous to the current Neo we saw, as proved by the various television monitors in the Architect's room- which thus represented the reaction of the other Neos upon talking to the Architect themselves. But within those last 5 events, Zion was destroyed and all those other Neos failed. However, like the Architect said, he just rebuilds (correct me if I'm wrong) the Matrix once again, and in some ways, "better" than the ones before it. But, as with all things in life, the essential program of the Matrix has it own byproducts- in this case, the humans who find out about the machines and thus go against it (which also somehow leads to the re-construction of Zion). So, the Architect waits expectantly for "The One" to return and expects him to make a choice- not exactly the same one as before- but a choice all the same. So in many ways, the life of the Matrix and the people of Zion can best be described as a cycle, or loop, (at least within most of its lifetime).
Then with the whole prophecy thing, the sole reason the Oracle ("mother" of the Matrix?) was created was to serve under the Architect (though I can't remember for what reason). Eventually, however, she sided with the humans strife against the source and the machines, and soon created the "Prophecy of the One" to give the renegade humans some hope for their cause- but it was all a lie, as Neo said, since even false hope was suffiecient enough for the people to live on. And as we saw, Morpehus was especially crushed by this reality, as he based his entire life's work to the fulfillment of the prophecy. [Now this is where it gets kind of confusing, since Neo still has unforseen powers and incredible strength, and can supposedly transfer this to the real world; despite the real truth about the prophecy.]
But the whole point of the movie, as I think it is, was to witness that "this" Neo chose a much different path than his predecessors- unlike the last 5, for his love for Trinity were much more than what the Architect perhaps never predicted, and so saved her from death through the use of his powers. The only question is, what now? Neo has already been to the source, like the Oracle told him to, and chose a different decision in saving his love rather than the people of Zion from the inevitable invasion of the machines. Meanwhile, Agent Simth has become a "rebel" program of sorts as a result of the last fight with him and Neo, transferring some of his powers to himself, and- as stated in this thread before- is no longer confined to the virtual world of the Matrix. With the infected person on board the ship in the last scene, Smith is closer than ever in killing Neo for reasons unknown; along with hudnreds of Smith copies awaiting inside the Matrix.
So it'd be very interesting to see how the story unfolds in Revolutions.