If you haven't seen "The Matrix Reloaded" then DONT read the rest of this article. If you HAVE seen it, then here are my thought's on Neo's meeting with "him". Spoiler alert
Ok. Obviously "him" = "The Architect". So what are the thoughts? Simple. The Architect says to Neo that he (Neo) is the sum of many small anomolies inherrent in the Matrix. Essentially (for the non- mathematical) if you divide 3 by 2, you get a remainder of 1. Neo is the 1.
The Architect, also tells Neo this has happened before and in fact there have been several "Neo's" and "Zion's" and all have followed the same fate. However "this" Neo doesn't follow the same pattern as the previous and decides to rescue Trinity and sacrifice Zion etc. There are several things that have led me to believe what I am about to say. If you've seen both the Matrix and Reloaded think about everything the Oracle has said to Neo, think about Morpheus, Trinity and the role of Zion. Think about what Agent Smith has said to Neo and the "powers" he has inherited in Reloaded. Think about what the Oracle said regarding rouge programs (eg, "The Twins" - do they rock or what?!). Now think about this: Neo is NOT the anomoly described by the Architect and the Oracle is right: without Neo, the humans are doomed; desite the apparent destruction of Zion at the end of "Reloaded".
So who , or what , is the anomoly? I propose Agent Smith. He fits the profile for everything Neo is. Smith himself said to Neo, in the "100 Smiths" scene, that when Neo "destroyed" him in first movie that Neo left some of himself behind. That is, the "new" agent Smith IS at least in part, Neo as well. In programming terms; some of Neo's code was "ported" to Smith.
So, kill Smith, and therefore zero the anomoly, the Matrix returns to an equilibrium, the humans live and the machines are defeated. Everyone lives happily ever after :-)
Or I could be completely wrong, and will look like an utter idiot when "Revolutions" is out.....cest la vie.