This entry presumes that the first change proposed in this list will never happen. If the Wachowski's do start work on a new Matrix trilogy and decide not to go with a prequel idea, then this is what their films should focus on i.e. the rebuilding of human civilization. We're shown only briefly in the first film what the remnants of the old human cities look like on present-day Earth, and while what we see is in fact a computer program, you can bet that the real version doesn't look much better. Without sunlight, the Earth's surface would be devoid of both plant and animal life, unable to sustain anything except inorganic organisms. We know that it was us that "blackened the skies" in an attempt to destroy the original power source of the machines, so if another film does continue on from Revolutions, we could easily see the narrative focus around human efforts to clear the eternal darkness, thus giving the machines back their original power source and ending their reliance on brainwashing humans.