There are still some questions I have:
Is Zion the real world? Or is it a backup matrix that the machines created to control the 1% outside the matrix?
If Zion was the real world, then how is it that the machines can correlate the actions of the real world to that of the matrix? For example, during the highway scene, Morpheus is about to fall off the truck, but at that exact moment Niobe catches him. How did the machines know that she would be there at the exact time? She is not part of the matrix, therefore, her actions cannot be predicted. So if let's say the operator of the ship gave her the wrong directions of Morpheus' location, or was distracted for 5 sec. Then she would not have been there at that exact time when Morpheus fell, and he would have died.
In another example, how would the machines be able to send a Sentinal to kill the ship of the crew that was to take out the backup supply, therefore forcing Trinity to replace them? The Sentinal killed the crew in real life. How can the machines plan this out if they have no control in real life? (if the Sentinal was there ten minutes later, they would have succeeded in taking out the power supply and Trinity would not have to enter the matrix). Furthermore, this had to be planned out, because Neo had the dream that Trinity was going to be there (taking out the idea that the Matrix adjusts to mishaps).
Also, going back to the first matrix movie, Cipher is killed by Tank just before he was going to kill Neo. Coincidence?Obviously, the machines don't want Neo to die, since they want him to go back to the Source. So during the dinner with Cipher and Agent Smith, why didn't Smith just kill Cipher if he knew he was going to kill Neo? It would make sense if Zion was a backup matrix, and the machines did have control. Then Smith would know all along that Tank would kill Cipher, thus he doesn't have to worry about Neo dying.
If Zion was a backup matrix, then that would explain nearly all the coincidences and loopholes. Except for the part where Neo has to save 23 people and rebuild Zion.
This would explain why Neo can disable the Sentinals at the end.