Personally, looking back after eight years, and going through all of the old stories on the website as I've been re-posting things to the blog that I'd lost when the server crashed, it got me thinking again.
Now, I did find an article I had written about why the Matrix Revolutions ended the way that it did. http://www.matrixfans.net/the-end-of-the-matrix-revolutions/
It sounded very logical, and in fact, if the Machines had continued their route of Zion, all of it would have been destroyed. (Likely save for the number of survivors needed to rebuild the city.)
I think, if I was making the film, I'd start by re-configuring The Matrix Reloaded. I'd wipe out the pointless rave and sex scenes entirely. They have no bearing on the overall story, and mean nothing. They also don't move the story forward at all, and that is wasted screen time. I'd use that extra time to begin providing some answers to open questions. Neo would be freeing people from the Matrix by the thousands. Zion, in the hundreds of years since the Matrix was built, will have an infrastructure that is capable of living all of the people that are being freed. That would be one of the twists in the middle of the film. I would also take part of that time to end the film with a cliffhanger that lands like a firework. Something that makes people talk, not something like "Agent Smith is on the table next to Neo, OMG." Neo would have the same powers in the real world that he does inside the Matrix. In fact, not just the same powers, but also the ability to EMP blast Machines.
I'd then start Matrix Revolutions with Neo, now empowered, would enter the Matrix to free whomever he can, while avoiding the hundreds of thousands of Agent Smiths that roam the world.
As Agent Smith takes over a new mind, the Matrix begins to respond by unplugging those people. It's brutal and diabolical. This elevates Neo into the hero we all wish he'd been, as he rushes to free as many minds as he can. As the Machines are unplugging people, less power is getting into their systems, and they begin to fail. Parts of the Matrix are now glitching. Agent Smith is causing the Matrix to collapse on itself in his mad rush to replicate. Neo can still destroy Smith in the same way as he did at the end of the first film, and continues to do so. Each time, however, begins to take a toll on him and makes the other surviving Agent Smiths stronger. Finally, Neo realizes that he's out of time. There aren't anymore lives to free from the Matrix, and he needs a way out. There's one hardline remaining that works, and he has one final battle with Agent Smith to get there. The fly throughout the Mega city, battling in the rain and Neo finally gets to the hardline and exits the Matrix.
At this point, Smith shouts, this is my world! My WORLD! as he does in the film, and the Matrix blinks off.
It's going to start a very long reboot sequence.
This was all part of the plan. Neo is now flying toward the Machine City of Zero One. In doing so, his speed causes a break in the polluted sky for the first time in hundreds of years. When he arrives, the Machines are ready for him, but he is too much for them. He manages to shut down the defense systems long enough for Zion's fleet of hovercrafts to launch a full assault against the machine city.
Finally, Neo is able to get to the prime machine, the Deus ex Machina, as we saw in the film. Only this time, the deal is different, and the Machine leader uses machine logic so that it will survive alone, but that is what Neo needed to infect it with a virus. The very same one that he had sold at the beginning of the first Matrix film. (So that's what it was!)
In the end, humanity is free, and natural life starts to rebuild without artificial intelligence to fight back or enslave us.