So in previous Iterations......
Did Neo Enter Smith in the Hallway in M1 and destroy him in the last version of the Matrix? Did Smith kill Neo there in Previos Iterations? Did Neo kill all the Meros henchmen in previous versions? and if he did do the Machines replenish the Mero's supply of Rouge/Vampire/Werewolf Programs? If so than I am really REally buying into EvilDead's theory about Rouge Programs not really being Rouge at all, just appearing this way to our Pawns, The Humans! in order to further control the humans the Machines installed these rouge programs that appear to be on humanities side but really all lead the humans to the point the machines want them to get to!! hmmmmmmmm