Wow I was always confused by the ending of the last Matrix movie how Neo did what he did, now I must look up peoples ideas of what the ending really meant.
Instead the movie baked in religious overtones and went the supernatural route (basically invalidating everything they set up in the universe in the first place).
Interestingly, the Thirteenth Floor did a pretty good job of that overall premise (sims inside sims), but without the dystopian overtones.