The long rant of my review short: The movie was enjoyable, although I failed to be impressed. If any of you have read Scott Kurtz's (of PvP fame) review, I agree with most of his points, although I did manage to enjoy the film for the most part. I found myself bored during the 100 Agent Smith fight. It got repetative, and I could tell they were using CG a lot, and it looked it. Also, I think a lot of the effects would have looked better had they used wires, like in the previous film, and there were a few instances where the slow-down effect seemed random (during the exchange of gunshots immediately prior to the highway comes to mind).
The easiest explanation of how Neo was able to sense and stop the Sentinels in the "real" world, is that he didn't go into the real world. Instead, when he went into the mainframe of the Matrix, he entered a subroutine designed to mimic the world they new, only with the illusion of Zion being destroyed. As he's still in the Matrix, he can sense the Sentinels and control them.
Another explanation would be that the Matrix is a prison, in a more conventional sense than we are lead to believe. IE that for whatever reason these people were placed in a virtual world to keep them passive. However, the creators of this prison realized people could figure this out, so they designed a second layer to the illusion: that while World A is an illusion, the real world is one where they are beset by machines, who have created this illusionary world. The people who see through this illusion will feel that they've been able to see through the illusion, but fail to see the miserable world is also an illusion. Mainly because the idea of a world modelled on something tolerable and with a decent amount of security could easily be seen as someone's attempt at an illusion, but why would someone imprison someone else in a dystopia? With a dystopia, they have the belief that they are fighting against something that's oppressing them, thus channelling thier rebellion into a safe outlet.
I thought of this hypothesis after I saw the Matrix back in 1999, which was basically remembering my reaction when I was studying Buddhism years ago: IE If this reality is an illusion, how do I know the reality Buddhism teaches is any more real (and by extension how do I know Nirvana is real)? Granted I grew up reading Philip K. Dick, so I'm might be somewhat inclined to trains of thought like that.