apt101
Interesting point: At the very end of part 1, note that after a few seconds once the trace running begins as Neo begins speaking - the on-screen message reads "warning: carrier anomaly" - then there's the System Failure. The system reacted to what the Architect revealed in pt 2. This, then, lends itself to the Matrix having to be 'Reloaded' with Agent upgrades and program deletions (ie - Smith & the Oracle). Neo states that he knows they (the machines) are out there and that he can 'feel' them as he then stated right before destoying the squiddies in pt 2. Lastly - he goes on to say will pretty much destroy the Matrix and show these people 'a world without you' & 'where we go from there is a choice I leave to you' - so maybe this all foreshadows what eventually occurs in Revalations.