Hey, my first post!
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I have briefly looked at other theories so I hope this is an original contribution and not a rehash of older stuff. The basic idea is that the Matrix is a critique of modern society in the form of a metaphor. This will explain whether there is a matrix within the matrix.
To start: our current world = the matrix. This is where the majority of the people live their daily lives. They are fooled to believe whatever they believe by the system, which in the movie is represented by the machines.
The system abuses the unsuspecting humans by manipulating their believes.
Then there are underground groups that fight the system. In the movie we see come across one that has acquired enough power to withstand the system for now. The system knows there is an underground resistance group with enough power to becoem a nuisance so they start digging for information about the base of this group so they can infiltrate it and destroy it.
At the same time the underground group is looking to recruit new members who add highly sought after skills represented as hackers. With the use of illicit drugs they show new members that the world is not what it seems. Furthermore they come up with a religious story in order to create fanatic true believers for the reform they are after.
In the fight between agents of the system and the members of the underground some agents become so frustrated they create black ops, going to the extreme opposite viewpoint of the underground group.
This radicalising of the conflict puts too much pressure on the system. So that while one part of the system is still attacking the underground group, a second part of the system is trying to take over the system and a third part of the system is trying to bring in the leaders of the underground into the system in order to stop the radicalising. This third group succeeds and the system, a bit changed, continues to exist having taking the underground group in.
So as the system survives a new underground group rises to power and everything happens again.
It is not so much that Neo is a program, it is more that the programs are really people. Machine City doesnt really exist, it is just the center of power of the human system. Zion is just one underground group and after it's demise another one starts.
To answer the questions:
* The machines have powerful weapons and highly advanced machinery but have to dig/ fight Zionites for 100 years
While the system is powerfull it takes time before sufficient information has been dug up to destroy an underground group.
* and cannot get their energy from above the clouds?
While the system is powerfull they are still depending on the masses to continue their normal activities for the system to work.
* Why did the machines invent the Matrix simulation at all? All they need to do is to cut a few nerves in the brain to make the bodies helpless.
The system is dependent on real humans doing real labor.
* Why are most whites the bad guys?
The current system in control is run by white males.
* Why do the heroes wear sunglasses and leather?
Pure gloss? Stylish bloat?
This reflects the current underground fashion.
* How could Zion be destroyed and repopulated already 5 times?
Different places/groups.
* What happened with all the debris?
Incorporated into the new system.
* An important question dealing about whether Zion is real or just another rebootable simulation.
It is real.
* Why is Trinity Trinity? What's so three-ish about her? The Wachowski said that every name was chosen very carefully. Was it? She has a side role (who hasn't?) and dies.
To show how true believers use mysticism and symbolism without effect.
# Is Neo really dead at the end of the movie?
No, just incorporated into the system.
# Is the Merovingian dead?
No, just a previous underground leader incorporated in the system.
# What will happen with the girl Sati?
Maybe she will lead a new underground group to be incorporated later on.
# Are all humans dead after Smith took over them?
No, they are brainwashed by the lying & deceit of the black ops triggered by the rise of the underground.
# Has the refreshed Matrix any humans at all?
Yes, the new system prevails and people return to their normal lives.
# Neo sees everything in Gold Code
The underground leader starts seeing the purpose of the system.
# Energy bits are flowing (similar to the green matrix code).
idem
# He sees Smith with sunglasses in Zion.
The underground leader start to recognise that the actions of the underground have created a monster in the system itself that now threatens the human race.
# He can stop sentinels with his thoughts.
The underground leader, having come to reason seeing both viewpoints, is able to pursuade representatives of the system to let him continue on his journey towards the center of power to safe the human race (system and underground).
# A sentinel goes thru him.
idem
# He understands machines, knows solutions and foresees the future
The underground leader comes to reason: he understands that in order to stop the bloodshed and possible extinction of the human race he has to join the system. The system off course has known from the start that it needed to incorporate the underground leader to survive.
* Smith: "Do you like what I have done with this place?"
Hell, where do we see how the deterioration of the Matrix occurs bit by bit?
More and more people are duped into a radical political position.
* Where do we see how the system tries to beat back Smith?
The operations of the system are hidden from view, and they might not be able to control their own factions.
* Do we see how he takes over more and more people?
No, but suddenly Smiths are everywhere.
Political propaganda works that way.
* Smith flies now. Why? How did he learn it?
The political faction represented by Smith is really taking off.
* Smith meets Sati and Seraph. What happens then?
The system checks on former and future underground leaders but as they pose no threat yet, they are left alone.
* Trinity dies (much too long) after a few scenes. Why so fast? Why so long?
True believers are valueless.
* Morpheus is degraded to a driver's mate.
Idem
* Persephone has just 1 sentence to say.
Idem
* Link & Zee...what a boring couple. Even the relationship between Trinity and Neo is boring. The movie tries to hide it beneath theatrical music volumes.
Idem.
Now for a real life example (don't take it the wrong way, this is not what the Matrix is about, just a clear example of the general dialectic between the controling system and any underground).
The Matrix: duped citizens of Western countries.
The Machines: Bush, Blair etc.
The Underground: Moslim extremists.
Smith: Renegade CIA operatives
What is needed is a guy who becomes a leader of the Moslim extremist so that they truely believe in him to fight the US & friends. Then out of frustration CIA people start building an opposite faction starting wars (Iraq, Afganistan etc.). Now the Moslim leader needs to understand that he need to make peace with the US & friends in order to make sure that no World War erupts from all this.
Proto
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