My only real gripe with the matrix trilogy is where Neo can “see” agent smith in Bane’s body and “see” all the machines at the machine city. It didn’t need that over the top messiah thing when he was already the messiah simply because of his power within the matrix.

And if the idea is “the real world is also a simulation, made to convince humans they were free” it sort of goes against all the monologuing that smith and the architect do about how humans rebelled against versions of the matrix in which they were free