But how do you know its over? Where in the film is it certain the war is over? Except for a kid who sees the squiddies turn tail and gets happy and does a Jimmy Stewart from "It's a Wonderful Life"? And back to Matrix Online, if its over there would be no story in the follow up game. And then the whole thing about "Will we see Neo again?" And the oracle replying with something like "Probably" means that there will come a time again when things heat up again and people will need him again. Or actually, people are not happy and he emerges from their discontent which was pritty much the boiled down reason the architech gave in the 2nd movie.
It just seems like they couldn't tie things up because the matrix seemed like too much of a good comodity for WB and probably forced the brothers with lots of money to leave the end open for later developments. I'm not specifically saying films, I heard they wont make any anymore. But IE books/games/comics/anime series/collecting cards/cereal you name it. Its just how the business "over there" works nowadays.