»Why Zion is just another Matrix, point 1.«

"Neo 'saw' a golden code Sentinel that goes through the ship without damaging it, then 'absorbed' by Neo, then Neo knew the only way to beat the sentinels is by going up above the cloud."


What happened in this scene was similar to what happened at the end of Reloaded. Neo didn't seperate his mind from his body, completely, but he did enough so he could absorb the sentinel instead of the sentinel hitting the Logos and having something disasterous happen to them before they could reach the machine city.
The theory of a matrix within a matrix was shot down in the very beginning of Revolutions. Neo didn't stop the five sentinels at the end of Reloaded because he was in another matrix, yet because he seperated his mind from his body.

The MWAM Theory was never shot down. The majority of the Matrix fans just ganged up on anyone who believed it. It became taboo to speak about it, but all of the evidence remains and has never been discredited.

Instead of shooting down MWAM, Revolutions opens with a code sequence that shows a shot of the machine city that pulls out to reveal that it is INSIDE of the green matrix code. Then it goes on to add even more clues - as discussed on this thread.

It's fine for people to reject MWAM for whatever reasons they choose, but the evidence remains and increases with each film in the trilogy.