Having spent all morning reading this.. (saw the film last night)..
On the film: Good but not great. Despite the plot, large chunks of the acting were awful. Totally uneeded scenes ( Oracles defender, rave scene, love scene). (By the way, standing that close to molten lava would require SOMETHING on your feet)... Some of the fight scenes dragged (some of the cgi wasnt' that great).....
As someone pointed out it just lacked the "coolness" of the first (and also the score didn't help).. Those are just editorial / dicitorial points..
Regarding the plot, I thought the matrix is run by the machines. It is not the machines themselves. The agents are merely software programs that exist within the matrix. That being said there must be some kind of feedback, which detects these anomilies.
Why they don't kill the humans the fall into the .1% not fooled? What purpose is there to keep them alive, unless it is deliberate?
In the first film we saw a machine come and check out Neo when he woke up... It should have just killed him. Acceptable losses. There is no need for any 2nd matrix, secondry systems, control loops etc. You fit the program so that 99.9% believe it, those that don't you kill.
That is my first big stumbling block. That is the logical thing to do, mince em up feed em to new grown babies and get on with it.
As for Neo being inserted into the source. what source? The software? How does that work, He may have been deceived by software but he is not software he is human. So what does that mean.
My explaination is that if the machine are intelligent and concious, then they need things to do. In a perfect matrix, with all anomalies sorted they are bored. They exist and perputuate for no reason. That screws up their logical world. They need purpose. They deliberately allow the matrix to be flawed. It's a game.
That aside I hope agent smith does turn out to be the anti-hero.
No idea how Neo stops the sentinals, I hope it's NOT a 2nd Matrix as that is a bit poo. But I also hope he's not got some "mystical" ability either.. How can a software program, affect physics in the real world? I hope there is a third option....
Az
P.S. Lot's of this is rubbish..