Other than Neo Stopping the Machine Weapons, Are There Clues the Real World is Another Matrix?

My question about Neo stopping the Machine weapons got me to thinking, since both answers (so far) have brought up the point that "reality," in this case, is just another matrix.

I never really gave the sequels much thought, since they weren't as compelling to me as the first movie, but now this has me wondering.

Are there other clues or indications that the real world, the one with Zion, is another virtual reality? Is it possible that the whole concept of using humans as a power source is inefficient and won't work well a clue? (Or is it just an underthought justification for the machines keeping humans alive?)

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(Note: I know this asks for something that may be a list of items, but this is a finite list. I've discussed that with moderators who feel there's a difference between an open ended list and one with a limited number of possible items. Please don't add "Me, too" answers with only one item.)

Answer

1. The Architect's claim that Zion is just another form of control.


2. Councillor Hamann's comment about Zion being dependent on machines may have been a hint to Neo.


3. The fact that the machines do not chase hoverships or drill more often or with more determination. They had a massive swarm of machines at their disposal (which they finally used on the assault on Zion), but they never send multiple waves after an EMP-armed rebel ship. All it would take is for the second wave to wait out of EMP range.


4. Only three agents will engage rebels at any given time.



5. The machines never allow the agents to load larger weapons (e.g. chain guns), vehicles (helicopters) or even more ammunition (Smith's empty after the subway shootout). Agents are probably not even privy to the possibility that Zion may be a simulation.


6. Neo re-entering the Matrix without a cable. So there is a data flow between the "real world" and the Matrix that is not dependent on a jack.


7. The "real world" is extremely unpleasant. It almost makes you want to stay in the Matrix. This could be a deliberate attempt by the machines to make it unattractive to all except the most malcontent.


8. Smith's ability to download into Bane's brain. The interface accepts sensory data from the Matrix. How did an entire person's worth of data get downloaded? How was Bane's brain rewired? The interface as we understand it cannot do this.


9. Injuries in the Matrix translating to injuries in the real world.


10. And as mentioned in the linked question, Neo's ability to see the "real world" in another code-like view (except this one is yellow).


11. The fact that the residual self image resembles the person's "real world" appearance. See this question.