Yes, an analysis on what The Matrix Trilogy was about is 7 years late. But like most computer geeks, The Matrix blew me away when it came out in 1999 and I still think about the series. The 4 year wait for The Matrix Reloaded & The Matrix Revolutions in 2003 was the most agonizing sequel wait since Return of the Jedi.
Like a lot of people, The Matrix trilogy felt like it declined in quality and satisfaction as the series went on. I've watched all three films numerous times, but I recently did so again since I ripped the Blu-ray's to H.264 720p HD. I wanted to finally put to rest for me what The Matrix Trilogy meant, to finally find peace, and I think I have.
What Did It All Mean
*** Spoilers ***
After watching the films again, google revealed these essays which nail probably 95% IMHO of what is going on in the story:
The Matrix: Reloaded, Explained
The Matrix: Revolutions, Explained
Short version: The Matrix Trilogy plot fundamentally becomes the plot of Star Trek: The Motion Picture. To recap, in Star Trek TMP, VGER returns to Earth seeking the creator. It doesn't know that humans are its creator, only that the creator can be found at Earth's coordinates. But VGER, which is a Voyager probe from the early 1970s, as a pure machine has learned all it can in the universe, and wonders if it can become anything more. VGERs theory is that it can evolve further by physically merging itself with its creator. For VGER to become whole, both the logical and the emotional must become one. Ultimately, VGER and a human merge into pure energy and "disappear" from the known universe.
The Matrix Trilogy ends up being about the same idea. Two separate halves, man and machine, unable to evolve without the other. When you strip away the religious symbolism, kung-fu, and special effects, the real plot is that simple. Of course, machines are in total control of the situation. They've attempted numerous times (read the essays for an exact count) to build a better Matrix, and finally succeeded with the iteration we find in the start of The Matrix. This keeps most humans under control, but they block that doesn't accept the simulation always break off, and then the machines kills the whole group and start over. The machines have decided at the end of the trilogy to try a new status quo, with humans that want to be out of the Matrix freely released, letting those in Zion live without interference, and learning from humans the ability to make choices. They achieve this goal by integrating "The One", guided by choices made for love, into "The Source", and thus starting a new age of man/machine evolution. To be even more clear, machines have decided they have stagnated without better understanding and learning from humans, their creators. Just like VGER.
Of course humans are still completely subjugated by the machines and could be destroyed at any time, but at least its better than where the trilogy started!
Does The Story Satisfy?
The Matrix was a very satisfying story because it showed humans rebelling against a heavily machined existence which for a lot of viewers feels like their real life. The end of The Matrix promises a super powered Neo freeing humans from the machines like he was.
So what happened in Reloaded and Revolutions? My going theory before discovering the essays was that Zion, really the whole "Real World" was another matrix. The essays call this the Liar Theory because for it to be true, nearly the entirety of the trilogy is a big none of this matters because the machines are totally in control of the situation, there is no hope for humanity.
Instead, we are left with a smidgeon of hope that humans could ever defeat or live peacefully with the machines. No great rebellion, no turning the tables on the machines, humans only survive this version of the Matrix because machines have decided its in their best interest to evolve as intelligences!
Sadly, even with a much better understanding of what the story actually was, it wasn't what I expected and I can't claim it satisfies. Now as for the movies as entertainment instead of philosophy, sadly the sequels also fail
From Innovator to Stagnator
When The Matrix was released, part of the rush the film delivered was not just the exiting story of rebellion against machines, but the innovative use of F/X to better explain the story. From bullet time, to slow motion kung-fu wire work, to a lot of audiences, it was a revelation.
What did we get in Reloaded & Revolutions that was truly new, not seen in The Matrix? Really not much. We saw the burly brawl, with some bad at the time CG actors, Neo flying in the best Superman impersonation that we haven't even seen that character deliver yet, and well, nothing more is coming to mind. There seems like so many things they could have done in the Matrix. Neo could have flown so fast time could have actually stopped. He could have teleported, how hard is that once you can control the system. In short, Neo shows no imagination about what he can do in the Matrix once he can fly. The people that are free but in the Matrix doing stuff could have shown more skill, become more enlightened, just by seeing Neo do all the crazyness he could do. Why not show bits of code coming off agents as Neo hits them? Why not explode them into code when he has won a fight? It just seemed like once you had control over the code, they could have kept ratcheting up his powers. I know though, that's not the story the Wachowski Brothers told or perhaps wanted to tell, but it would have been more satisfying because that is perhaps what was expected after the end of The Matrix. We certainly didn't expect to sit through a huge number of kung-fu battles that result in draws. Just felt like padding, and don't even get me started on the mechs shooting down sentinels for like 30 minutes.
Conclusion
Warts and all I still enjoy The Matrix Trilogy because of its complexity, there are some great special effects, and the ideas of man overthrowing machines they have lost control of. I just wish they told that story in the sequels instead of seeing humanity under the machines control, only slighty less of it.