guesses about what is going on (spoilers)

Rating: Null/10 (18 May 2003)

The Matrix is a mystery story. A good mystery story is written with enough clues that it is possible to figure out the mystery before it is revealed. Assuming Matrix is a good mystery story, here are my guesses.
The matrix needs to stop Neo so it can destroy Zion. It doesn't need to kill him, it just needs to occupy him for 72 hours. A technology is devised that allows people to be hooked into the matrix without them being plugged in via the usual cranial probe. This technology probably involves nanoprobes and is transmitted by physical contact. When the compromised man shakes hands with Neo, he transfers these probes to Neo. Neo is now primed to be reloaded into the matrix.
For this reload to be convincing to Neo, it must continue Neo's life in a believable way. With his unique abilities, once reloaded he will be able to sense things that he cannot sense in the real world. Thus the reload point must occur sometime after the handshake but before Neo's first feeling that "something is wrong." I did not watch the film with this in mind, so I do not know when the reload happened. A viewer looking for this will probably find this point.
The upshot is that all the doubts engendered by the Architect are unfounded. It's just the matrix messing with Neo, keeping him busy and off balance. Keeping Trinity and Morpheus under constant threat helps too. But in the end, Neo blasts his way out of the reloaded matrix.
As a failsafe, I'd guess the nanoprobes now will try to incapacitate Neo. So Matrix Revolutions may basically be a pitched battle for Zion, with Neo out of the action until the final moments, when he swoops in and saves the day.