>>212319212My personal, unfounded theory, is that whatchomsky got a hold of the script they wanted to do without him, and it was actually worse
Extrapolating from matrix 4, I would say they wanted to make a movie in which Neo was crazy and actually never went to the matrix and it was all a dream, trinity didn't exist, and it was just him all along. Possibly having a black kid helping him recover, or hinting that his crazy can be passed on and there could be other Neos or a new girl with his crazy or something they can do with new actors.
Because the movie is the complete opposite, it reinforces the matrix, confirms that everything was real and happened, that all the characters were real and the end is open for more "matrix" storyline and hard to bounce back into something else.