I will make these bets/predictions (in October, let's see how close/far I was):
Zion is not real - Zion is a part of the matrix. If a human mind cannot accept the consensual reality that was the primary matrix, then the mind will not participate further (either madness or coma?) and will be a waste of flesh for the machines (e.g. no to low power output). To combat this, the machines built another layer. One of escape (or error trap for those machines here). To those who reject, the machines built a false explanation. The human mind accepts the reason and goes on. However, there is a break point to this acceptance. A quarter or a million people now reject the false matrix and believe in this high matrix (matrices?). Morpheus says in his pre-rave speech that he rembembers 100 years ago when this began. 100 years (+ his age) old? Hmm, he might be speaking metaphorically, but...
Who is "human" and who is not - The councilman (played by Anthony Zerbe) is not. Morpheus is not. The inhabitants of Zion and the first matrix - I'm thinking 50/50 here. Reason: The machines need to understand their creators, humans. There is a symbios at work but I think the human side is waning (dying off). The machines are willing to live underpowered but they want to be "alive" and exist like the humans do/did. (Some of this comes from "The Second Renaissance" Animatrix episodes on the web.) Thats why the councilman preaches caution and co-existence to Neo and to show him the underbelly of Zion (machines behind the curtain so to speak). Morpheus is a program to move along the plot. Of course, if he is real, then the Zion matrix has programmed him to be a zealot.
Programs, programs, programs - the architect wants there to be a believable matrix and zero defects. the french guy, oracle and keymaker are minor programs within the larger system. At one point they may have been system administrator programs (regulators) whom have jumped into the matrix as sentient entities. That's why they survive reloads because they can enter the hallway of doors (e.g. slip back into the mainframe/main program). However, because they are minor programs they cannot see beyond their program. They can do awesome things within the matrix, but basically are stopped at that level. That is why the french guy keeps yapping about "cause and effect" because that's all he can do. He sees interaction at the most basic controlling level. Same with the oracle, make a pronouncement here and there and then follow results.
Neo and choice - in the room with architect, Neo sees himself in all those monitors - which are mathmatical representations of probability. Each one is a probability that the architect computes. At that space/time moment, Neo becomes one of the probabilities but not all the time. It's like the architect is running "IF - THEN" logic statements at a human. The architect says Neo carries within him the key to solving this program. The architect has programmed other iterations of the matrix but have all been flawed. The oracle in the last iteration began to see the glimmering of the "human equation" which the new matrices must include for the architect to succeed and in this present version the architect has built the Neo equation. Everything that has come (in this version - Morpheus getting him, Zion being built, etc.) before were pre-reqs to the Neo equation becomming active (needs a backstory that Neo can understand and believe before he makse his "choice".) If you notice, the probability Neos all made the same choice (walk to the Martix door) as did the one Neo. The architect is betting that this solution will somehow make the program work (full human/machine symbiosis). The architect can only make probabilities and understand permutations of choice but ultimately cannot create an outcome unless the humans actually participate.
The next movie - We only hear, not see, that Zion has fallen. Yet in the trailer (which is different than the one I downloaded) shows some of the "Metal Gear" type of guys fighting. If only one ship survived the whole distruction, then where does this guy and fighting fit in? I think the Agent Smith program stowed away on the ship and was able to infect them all once they emerged from the matrix. Zion may still be functioning. As to Agent Smith, he is not bound by traditional program routines. By being restructured with Neo routines added, it becomes Neo-lite. Program with higher IF/THEN statements and boundaries. That is why is was able to slip into the door hallway. Now, the program has gone rogue and must be dealt with by the Neo solution. Hmmm. Agent Smith representing task/master/authority program; Neo represents symbiotic relation/merge?
Coma with both? Naw, think reloading...