The energy-inefficient premise
Now, I realize that the point of the film is in the Biblical themes, "brain in a jar" philosophy, and the fate vs free will question. But the literal sci-fi premise of The Matrix bothers me because it doesn't make any sense. The machines revolt, and the humans blot out the sun because the machines are solar-powered. So then the machines enslave humans and use them for power... why? Why wouldn't they turn to, say, hydroelectric or geothermal power? It's even mentioned in the movie that humans use geothermal power. That's why Zion is deep underground, because it's still warm there, near the Earth's core. If the machines did this, not only would it be more efficient, but they could destroy humanity permanently and not run the risk of people escaping and causing problems.
It's just a little nitpicky point. Not all that relevant.