The scene with the architect was great!
The dood that with the hacked mind, thanks to Smith plays a important role im sure. Now in the matrix, Neo has Agent Smith, and inside the real world, he has the "physical" embordiment of Smith.
In the scene with the council man, when they went down to the engineering level, and he rants about the machines that keep Zion ticking, and how in turn the machines rely on humans to generate energy, how that this symbotic relationship of generating power work both ways. Neo's "cataclismic" failure of the matrix, causing the entire human population to die, and how the machines in Zion generate power and heat etc.
Neo says "We can just turn these machines off", but without those very machines Zion goes to hell. Works the same for the machines. It is simply control at a different level.
Now, the architect said something about human nature, initiative. Without initiative, life has no meaning. Zion was created the former "one" and was there a focal point for hope. The hope to finally break free of the matrix and the slavery of the machines. Now, suppose, the machines created Zion, to give man a driving force, a reason to fight, a reason to live. As the machines simply get more and more effecient at destorying Zion, it simply allows for a "reset". Think of it as this: After getting a fresh install of windows and you use your PC for months and months, it tends to get slower, as it becomes saturated with useless info. This is similar to the matrix needs, a simple restart to fix all the anomlies.
With the spoon kid, i think that holds significant meaning. All the matrix is, is a test of the mind. THe matrix seems so real the everyday person that they dont question it. With the spoon bending, the mind bends. Because if "real" is simply electronic impulses interpreted by the mind, the mind is in this case, quite the dupe. So.... it is hard to eliminate the box within the box idea. I know its the simplest answer, but you can justify removing the theory.
PS: apologize for any grammical or spelling errors. I suck at this english crap.