A little known fact is that they ended up virtually rewriting most of Revolutions after Reloaded's Architect section turned out to be the worst bit of the film. The original Revolutions expanded a lot more on the "sixth" idea, revealing that the Merovengian was actually one of the previous Ones who had rejected the whole system and chosen to live a selfish existence within the Matrix, and also had a better explanation of why Smith went out of control this time. (the theory being that the events of the first film were scripted by the Machines, all the agents effectively being actors/puppets, again giving the illusion of choice. Smith had "died" so many times his program became corrupted and literally ejected himself from the Machine mainframe, becoming sentient. They instead chose to make it that Neo overwrote Smith's program with an element of himself, which made the system unstable, so Smith's growing power was the system trying to balance itself. Shit idea, really)