Given the "loop" nature of the Matrix universe your edit sides with, it would be nice to see the moment in the train station when Neo runs out one side and comes back in the other - it's a good metaphor for the series and a foreshadow of your ending. Maybe Neo could dream that? And excuse me if that shot is in your edit, I don't remember it but maybe I missed it.
I did take that scene out, mainly because I had taken out the proceeding scene with Trinity, Morpheus, and Seraph driving in the car (which I removed because I felt it was an unneeded scene) and there were no longer any scenes to act as an "intro" buffer to the Neo's loop scene.
(although to be honest, I never really cared for that scene to begin with)
Originally posted by: Mojo_LA
Personally, I think the W brothers had probably planned that the big twist would be that the "real world" was a Matrix within the Matrix, the idea being that if people BELIEVED they had escaped, they wouldn't look any further. But I think since fans were predicting this would be the case, the film makers abandoned that idea just to avoid being predictable.
I think the bigger problem was that the filmmakers (or the Studio, for that matter) wrote the sequels based on what they thought the audiences' wanted to see in the films.