6) Again, that's one theory. An alternate theory is that the Wachowski brothers are frickin abysmal writers who just got lucky the first time.
You could also be generous and concede that they may have been okay writers but that in attempting to visually convey extremely sophisticated philosophical concepts using the language of cyberpunk mixed with the visual themes of martial arts cinema and work like Ridley Scott's Blade Runner their reach exceeded their grasp.
It was relatively easy to frame a story which posited Machines=baddies, humans = goodies in The Matrix but in Reloaded and Revolutions they moved towards a philosophy in which Smith became representative of a kind of nihilistic instinct where Neo represented a vital and enlightened soul, alive to suffering and the transience of the apparent but able to move within the world of appearances in tune with the creatures of spirit. The machine world came to represent this world of spirit over the course of the trilogy, programs and machines representing the highest forms of intellect and wisdom that much eastern philosophy attempts to teach us are, at first, seen as enemies of our unenlightened selves but later come to be angelic beings prompting us to move into a state of nirvanic bliss.
It's an interesting philosophy but not one that anyone has ever really tried to put into the visual language of action cinema, until these guys. That they failed was almost inevitable. That they tried remains admirable. That they are scorned remains unsurprising.
I have a theory that it's impossible to prove anything, but I can't prove it.