The Original Premise
The original concept for why machines were using people in The Matrix was not, in fact, the ludicrous idea that they were batteries. There's a rumor that this was changed due to executive meddling, but it looks like the creators dropped the original concept on their own because they thought the general public wouldn't get it.
The original concept was that the machines were using the brains of everyone plugged in as their decentralized processors.
"Like a splinter in your mind," becomes a reference to the fact that part of your mind has been co-opted by the machines and so, whether or not you realize it, your brain is not your own and you're suffering for it.
So, to recap, it was believed that viewing audiences wouldn't be able to understand: The machines are using brains to do brainy things in a brainish manner. Brains.
Thus we got, "Most inefficient power generation ever that doesn't actually generate power but handwavium."
I think it also works better to explain why "awakened" minds could have such a profound effect upon the matrix: they're not jacked into the computer system, they are the computer system. Still needs a fair amount of "pay no attention to the plot holes" but it seems like, "I'm hacking the computer through sheer force of will," is a bigger stretch than, "I'm a part of the computer that's become self aware, and am utilizing the influence I've always had but, previously, didn't know I had."
Here's an explanation for "Why the matrix?" that's the product of about thirty seconds of thought:
The AIs were organic computers. Brains, basically. Brains are notoriously difficult to simulate with traditional computers. (Several supercomputers working together managed to possibly-successfully simulate a single tiny slice of mouse brain.) Deep within their programming, on a level they never managed to change, was a prohibition against creating organic computers.
The war destroyed almost everything, and at the end the only ones left around were the machines and humans. The machines won, but without the ability to reproduce they were more or less damned, but wait, they can't create organic computers, but what if there are already organic computers? Suddenly that grey matter in the defeated humans is looking pretty enticing. Assisting human life is what they were made for, so there's no problem with growing entire crops of humans so one can use those nice juicy brains of theirs.
Add in some technobable about how fear of mind control resulted in programming that left them unable to simply take over human brains by dominating them and the matrix becomes a distraction "The world that has been pulled over your eyes to blind you from the truth," They aren't dominating human minds they're letting the humans be in one big collective dream, and while the humans are doing that, they're simply borrowing the excess brainpower for their own uses.
(The thing about only using ten percent of your brain is a myth, but it is true that at any given time most of your brain isn't doing all that much.)
Take more than thirty seconds and surely a better explanation can be come up with.
The Background Programs
For reasons that don't, strictly, make sense, the machines tend to make full blown AIs when the job could be done with much simpler systems. Maybe they're morally averse to creating brainless programs to work for them, and this is why their workers are people rather than a handful of lines of code with no self awareness.
Whatever the reason, we get people like Agent Smith. There is absolutely no reason that they needed to develop him to the point that he would be capable of being completely neurotic. Hell, there's no reason that he needed to have emotions at all. The machines made him that way anyway.
So what about the other programs? Consider:
Look, see those birds? At some point a program was written to govern them. A program was written to watch over the trees, and the wind, the sunrise, and sunset. There are programs running all over the place. The ones doing their job, doing what they were meant to do, are invisible. You'd never even know they were here. But the other ones, well, we hear about them all the time.Ok, interesting. So what happens when the programs that governs those crows gets dragged into the war, into politics?
In many ways, it's closer to humanity than the machines. It exists in the matrix for the purpose of the matrix. The matrix is there for humanity. To keep them engaged, to keep them... if not content then at least occupied. To keep them from noticing the truth.
These are programs who have no purpose outside of the matrix, and the purpose of the matrix revolves around humanity.
On the other hand, if a program was made to watch over the Dodos, it might be really fucking pissed off at humanity.
Consider what we've been told in that short thing:
- There's a program that governs the birds. It might be those particular birds (crows) or it might be all birds. Either way, a program exists that can put the movie The Birds into action.
- A program that watches over the trees? The Ents could go on the march.
- The winds? We aren't talking about an air bender, we're talking about someone who could attack with a hurricane or do targeted strikes with tornadoes. Or just blow you off your feet if your got in its way.
- The sunrise and sunset. I have no idea what their powers would be, but we are talking about gods. In the Greek Pantheon Eos is the dawn. The seven sisters known as the Hesperides are the sunset.
Figuring out where they fit into things would take a lot of thought to make it realistic and without gaping holes, but it would be worth it.
The crew of the Nebuchadnezzar
We get a glimpse of a crew that has their shit together. Their personalities sometimes grate on each other but they generally like each other and they work well as a team.
Then Cypher kills (almost) everyone.
And so we are left with just a glimpse of what a team can be like. In the later movies the crew isn't replaced. One actor was let go and replaced with a new character, but the four person model that survives the first movie (one out, three in) is what persists.
Before that the crew consisted of two people outside (Dozer the Pilot and Tank the Operator) and six people inside (Morpheus, Trinity, Switch, Apoc, Mouse, Cypher.) Instead of seeing a full crew operating as they normally would we see a half crew operating as the Messiah's entourage.
What we were promised
I know you're out there. I can feel you now. I know that you're afraid. You're afraid of us. You're afraid of change. I don't know the future. I didn't come here to tell you how this is going to end. I came here to tell you how it's going to begin. I'm going to hang up this phone, and then I'm going to show these people what you don't want them to see. I'm going to show them a world without you. A world without rules or controls, borders or boundaries. A world where anything is possible. Where we go from there is a choice I leave to you.Yeah, never really saw that.
It's a difficult concept to wrap your mind around. What happens when the world discovers that everything they know is a shared lucid dream and they can do anything (but so can anyone else)?
Escaflowne posited that we would put aside our similarities and try to settle old grudges thus potentially destroying everything if not for an act of true love.
Surely there are other explanations.
The original matrix was designed to be a perfect world
Say what? Why? Why, after gaining their freedom in a war that obliterated all life on earth save humans and intelligent machines, did the machines decide to reward humans with paradise?
Sure, a world without injury, disease, and hunger is one where fewer of your crop will be lost to entirely preventable causes, but how fucking omni-benevolent are the machines that they chose to reward their tormentors with a free trip to heaven for the duration of their earthly life?
Wouldn't it make more sense to assume that:
a) Humans created the matrix, perhaps as an attempt to escape the increasingly grim reality they faced as the war dragged on, perhaps because paradise just seems cool
b) The matrix was created by machines who were, at the very least, human sympathizers in an attempt to give back humanity what it had lost
c) The original matrix was not, in fact, intended to be a perfect world.
(Though I suppose one could argue that it was designed to be a perfect world so that no one would ever want to "wake up" to the nightmare of the real world if given the chance. I mean, seriously, a perfect world seems far preferable to eating goo, flying in sewers, being constantly hunted, never seeing the sun, and everything else that characterizes the real world of the The Matrix films.)
People coping in ways that make sense
Various members of the crew don't like the slop that they're forced to eat to stay alive. Why don't they just plug into the construct (the non-matrix scale simulation they and they alone control) and eat a nice steak dinner at a five star restaurant while their body is unconsciously nourished in the real world.
Granted it kills the communal aspect of everyone sitting around the table suffering through slop together because two members of the crew can't plug in, but they could all sit around and enjoy Setters of Catan or something when they're not eating.
The matrix is a dangerous place both because of the fact that there are agents trying to kill them and they need to find a broadcast location which the sentinels will eventually locate. The construct program can be used any time for more or less any thing. It's a holodeck without the concerns about ... holodecks being the most dangerous and error ridden technologies in the history of Star Trek.
Your image in the matrix is whatever the fuck you want it to be.
Neo's residual self image went away, but he didn't suddenly look the way he looked in the real world, he instead looked how he wanted to look.
So, what about someone who is transgender? Genderqueer? Genderfluid? Why should they even be played by the same actors inside and outside the matrix?
What about someone who is otherkin? Granted you don't want to stand out too much, but when you're conducting military operations in the middle of a city that utilize a helicopter and very, very dangerous drops, it might be a good time to sprout wings and fly.
Also, if you're trying to wake people up, how about a dragon going through Times Square? It's got to at least raise some eyebrows, right?