Clearly, the movies are about choice. Neo chooses to become the One, and he chooses to lead the attack on the Machines when the humans find out Zion will be under attack. The Architect says as much: about 1% of the humans chooses to reject the Matrix, and Zion is a 'steam valve' that takes the pressure off the system. As such, Zion is also a part of the much-hated Matrix construct.
But the machines are smart (they have to be if they want to keep the complete human population under control) and they have run simulations it seems. Neo is shamelessly manipulated by the Oracle. The Merovingian was not joking when he said that Neo was good in following orders.
But then we get back to the real world, and Neo stops several seeker-destroyer-machines (the large squid-like ones) dead in their tracks. WTF is up with that...? Then remember that the Oracle gave Neo a red piece of candy. Perhaps this is also a simulation? Time will tell, I guess.
That's not all. I have wondered about the nature of Agents since the first movie. As you all know, Agents can't manifest out of thin air: they have to take the place of someone who was already there. But what happens with the people they replace? Are they killed or is their consciousness somehow suspended? What do they perceive when they are being taken over? And what is up with not being able to manifest directly? What kind of stupid design decision is that? If I were to design a system that needed to be policed, I'd have omni-present and omni-sentient police programs that could kick your ass without even having to materialise. I'm sure the Architect could have thought of this -- but probably not the Wachowski brothers.
Neo supposedly 'freed' Agent Smith from domination (by whom? Who gives the Agents their tasks?), making him (literally) a free agent. Smith then proceeds to copy himself. Now, I can understand Smith copying his own set of instructions over the memory spaces occupied by another agent (it's all software, after all) but what the hell is up with Smith copying himself over humans? And what is with those humans functioning normally (but supposedly with the 'Smith instruction set') in the real world?
If the machines could do that, why didn't they just copy a minimal instruction set over every human in the Matrix and conserve some processor cycles? For that matter, why did they create the Matrix at all? I mean, if you can just 'grow' humans, why bother with their consciousness? Just lock 'em up and be done with it. Or make sure they don't develop brains or something like that (like the bioshells from Transhuman Space).
The nature of the machines is... puzzling. I've watched the Animatrix, and apparently the machines are sentient. As a cognitive scientist, I like that premise.
The tools rebel against their masters and defeat them in a final war. Fine. But then the machines spawn other machines. Do they gift these machines with sentience too?
Clearly some machines have specific tasks -- do they execute those tasks because they are made to like doing those tasks? Would that not make the machines that spawned him as bad as the humans? Doesn't that make the other machines think?
And what about those programs running amok in the Matrix? Suppose the Matrix is one big CPU, then all programs need their share of CPU cycles. Don't want a program to run anymore? Adjust the scheduler and the program 'starves' and be done with it.
Suppose each program in the Matrix is running on its own hardware. Don't want the program to run anymore? Either send those squid-like things to smash the hardware (they seem to enjoy that sort of thing) or simply disconnect it from the Matrix mainframe.
None of those (easy) solutions involves messy things like sending Agents after the hapless program.
Maybe I'm thinking too logically about this, but I just can't help myself. I always try to go for the most elegant, simple solution to a problem, and I can't imagine the machines would do it any different. And yet they don't. The Matrix franchise just isn't 'realistic' enough (in the sense of 'magical realism': the setting doesn't realistically flow from the magical premisse).
Still, it's a kick-ass action movie. ;)