My theory (SPOILERS)

Rating: Null/10 (23 May 2003)

This is what I've deduced...I don't know if anyone has posted anything like this, as I don't really read this message board often:
Every body hooked up to the matrix controls a program. Let's call it the "human" program. These programs have to follow the guidelines of the matrix (e.g. gravity, breathing, eating, etc.) To control outbreaks among the humans, special programs have been made (agents). To run a program, however, a human must have control over it, so the oracle, the architect, and any other human-like program are actually controlled by humans. The agent program can simply bend the rules of the matrix; they don't have any fewer restrictions than humans do, they just have the ability to modify the restrictions they have (e.g. they are able to set their gravity constant from, say, 1.0 to 0.5, or time from 12 fps to 24 fps ;-).
The agents also have the ability to wipe the human program from a human body and replace it with their own agent program. Thus, the agents have no real consciousness, they are just strict guidelines for how the humans that the agents jump inside should act. The agents are the only ones that do not have a physical counterpart, they are nomadic programs that constantly dwell in different human minds, which is why their features are so similar and plain (they're computer crafted).
Neo has a completely different program. Neo basically has "root" access--no restrictions or guidelines for how he should act or think. The only problem is that he has been living by human rules for so long, he doesn't realize that he can completely ignore the rules of the matrix, which is why he can only fly instead of, say, teleport, and why he has to terminate the life of an agent to get rid of him, rather than just delete him. These "commands" are well hidden in his psyche, and to use them would have to be a deliberate action. His first run-ins with his commands were in threatening situations (the first fight with Morpheus, the showdown with the agent, being killed, etc.). The reason why he has all access is because the machines count on him not being able to ever use them. If they were to give him slightly more power than a human, they would have to write an entire new set of guidelines and restrictions just for Neo, which would have taken a long time (and they might have been in the process of doing so...who knows?).
So because Neo is able to stop bullets and whatnot in the matrix, he gets the feel of how to do it. This is why he is able to stop those sentinels in real life. Imagine you had a third arm grafted to you, which was fully functional. You would not be able to move it because you do not know which part of your brain would move the arm, nor would you know how to stimulate the muscles that would control it. If you were hooked up to the matrix, and you were given a third arm, and a part of the program they hooked you up to was to have the ability to move the third arm, and you got pretty good at moving it about, when you got back to the real world, you'd be able to control the third arm perfectly (but for atrophy). Neo has been given the programming in his mind to control things in the matrix, so when he gets out of the matrix, he only needs to flex his mind to do the same, and he can. This plays along with the idea that within your mind is the ability to move objects and plant subliminal messages and whatnot, we just don't know how to harness it. Well, Neo was stimulated by the machines to harness it.
Morpheus and Trinity were not able to bend the rules of reality because they always figured when they could run fast or jump high in the matrix, it was simply because they were bending the rules of the matrix, and there was no thought in their minds that they could do anything of the sort in real life, since the rules in real life are steadfast.
Well, I don't think I left anything out. I dunno if it's going to be very harmonious with how the story is really going to turn out, but I think it's a pretty plausible theory.
Wyatt