I posted in the original revolutions thread that Reloaded wasn't good, but if Revolutions had gone another way, within the series Reloaded would have been great. There is a scene in Reloaded where the council leader was talking to Neo about control, and reality and machines. Neo is hating on the machines and the old dude tells him "What of those machines that reprocess our sewage--without them we'd die. We rely on machines every day."...To which Neo's answer is "we can smash them, we're in control". The guy kind of rolls his eyes a little and sighs at how humans equate violence with control.
Right at that point, I figured the story was going to head in a specific direction. I thought the Council were all machines, and Zion was actually a refuge for people who were rejecting the Matrix code, a place to rehabilitate them and give them what they needed (More conflict). I figured we'd see by the end of the movie that Neo was simply in another level of the Matrix (And sure enough, by the end, we see him take out the machines in the real world. So it was confirmed for me, but then Revolutions came out and didn't explain it at all.)
Anyway, I was hoping it would be revealed that mankind built the machines and created a utopia. The machines were loyal and worked tirelessly for man, their primary directive was to protect and defend humanity, and then obey orders. However, as mankind began expanding into space, a rift formed, and humans began ripping themselves apart through an ever increasing escalation of a great war. We eventually tasked the machines into the war, changing their programing to allow them to kill hostile humans--but the machines were sentient, and their original programming made it difficult for them to accept the new programing. Anyway, the machines realize humans will destroy themselves if this continues, and so they rise up--a classic Asmonov paradox.
However, instead of locking humans up and oppressing them, the machines worked tirelessly to ensure humanity was happy. First they built a paradise-like Matrix, but humans were unhappy, so they tore it down. Then they built the Matrix to try and create a space for humanity that could allow them to satisfy their violent urges without any actual risk. When you die in the Matrix, you're reset and start over--it's like a perpetual MMO. Neo and the others needed something more, so the machines made themselves the ultimate conflict, and 'played' with their masters to give them a purpose. In the end, Neo would learn this--he'd realize there was no way to get energy from humans; that in fact the Machines devoted mass amounts of energy ensuring humanity was well cared for. The machines kept talking about 'purpose' and how machines had to have a 'purpose' because they learned that from humans, that's why humans are so conflict driven, they need purpose. The machines created a world where their own purpose was being the perfect servant for humanity, giving humans everything they needed.
In essence the machines were God, they created world for man exactly how man needed it, because the hidden part of the story is man created God. That is why God can exist and be benevolent and still allow suffering, because in that final layer of reality, really, he's ensuring no one gets hurt, and mankind survives.
