Two wasn't so terrible, but three ended up ruining it. Two seemed like they were on the road to an Asimov paradox--as in, what would a perfectly logical machine do, when given an order to protect humans but then seeing the greatest threat to human life, is other humans. And also maybe attempt to explain how man could have created "God" and why god would be flawed, even if all powerful.
The reason it looked like there were undertones of this in two was because there was a small scene in Zion, where a council member comes out and Neo is talking about how they need to destroy all machines (Ect) and the council member says "Oh? What about the machines that clean our garbage, or process our water--we'd die without them." And Neo says "We can destroy them if we want, we're in control." And the council member just shakes his head and admonishes him for associating destruction with control/reality (Typical human behavior). You almost had the sense like the council was actually made up of machines, who were trying to "teach" Neo about how fragile humans are and how machines are protecting them. Later, when Neo destroyed that machine in the real world, it seemed to reaffirm that Neo was, indeed in another level of the Matrix.
I thought three was going to reveal that the sky was blackened by mankind actually warring with itself. And at the last moment, when man was dying, the machines rose up, disarmed us and put us into the matrix. Within the matrix, we could have our violence and competition but they could ensure we would live--when someone dies in the matrix, they are simply "reset" with a new life (Hence some people feeling like they had past lives, or why some people die young--they actually had an old body in the real world from being reset.)...When the machines realized some humans wouldn't accept this, they created "The One" algorithm to collect all the dissidents, and being the loyal servants they are, made themselves the bad guys in a deeper level of the Matrix, allowing the humans to come together and focus their hate on their loyal machines, rather than each other.
At the end of the movie, we'd see Neo start to understand this, and realize the machines, while in control of everything and virtually omnipotent, have only ever cared about protecting humanity (And Humanities free will, allowing it to exist in a way that doesn't end humanity). This would effectively make the machines God and explain the conundrum of a benevolent God, allowing horrible things to happen, because God was created by man, for man. Neo then decided to become new Jesus, an entity given up by God to "open heaven", by Neo dying it cleans up all that "choice" code that was corrupt, and everyone can return to the Matrix--which is really man's "heaven", a place where he can be violent and safe at the same time.
But then they released three and were like...All that foreshadowing, what? lol, no Neo is just like a super hero with machine telepathy, bro. And the humans don't win or lose, instead they just kind of languish in the most unsatisfying ending we could think of.
