I tend to think of the trilogy in the sense that Neo is always in the Matrix, he just thinks he is out, a la THIS , and then I see the second and third movies as being chock full of metaphor, like the Bible.
Makes for a much better viewing experience.
I read the "insane" fan theory but honestly, I'm unable to see the difference or why it should make a better viewing experience.
The only essential criticism presented here (please correct me where I'm wrong) is that Neo is able to stop the squid in the real world and that he became able to see in the real world though he was blind-folded.
For all we know Neo was or became a mutant with psycho- and telekinetic powers in the real world. Already in RELOADED we noticed that he was able to see into the future while in the real world.
Of course, such abilities would have have been incomprehensible for the machines just as it was incomprehensible for the Borg in "Q Who" that it wasn't Starfleet technology but the "Q Drive" that had brought the Enterprise-D that far.
He was an "anomaly" but far beyond what the Oracle and the Architect expected, thus able to accomplish feats considered to be impossible or felt by many to be exclusive to the virtual reality of the Matrix.
Bob
So you are saying that Q made it so Neo could defeat the squid and see even when he was blind?