It turns out the Architect's speech at the end wasn't just superficially designed to make you think it was confusing. It really and truly didn't make any sense. Here is a transcript of the speech, which is essentially the climax of the movie, where everything is supposed to be explained. Neo is given a choice between two doors, and decides to save Trinity instead of -- well, that's just it. Instead of what? If you re-read the speech, you'll find that the Architect is actually lying about the final choice. What he says doesn't make sense given what he's previously explained.
To re-cap: He basically tells Neo, to Neo's shock and dismay, that his journey is but a built-in corrective to keep the Matrix functioning properly. Just as in all previous versions of the Matrix, the One will "return to the source, allowing a temporary dissemination of the code you carry, reinserting the prime program," whatever that hell that means. But by the time the One does that, Zion is destroyed -- each and every time -- by the digging machines. Therefore, to ensure the survival of the human race, the "One" must always takes a group of 23 people "from the Matrix" (i.e. not from Zion, because they're all dead) and reconstitute and rebuild Zion. He does this because if he didn't, the whole Matrix would break down and kill everybody attached to it. Since all "free" humans were already destroyed by the digging machines, that would mean no more humans. So the One rebuilds Zion to ensure the survival of the human race, thus assuring the survival of the Matrix, and the whole process repeats itself, ad infinitum.
Of course the difference with Neo is that he loves one human above and beyond all of humanity. So rather than choosing to save humanity, he chooses to save Trinity, even though the consequences of that are (depending on which part of the Architect's speech you believe) either cataclysmic or completely unknown.
The architecht says: "There are two doors. The door to your right leads to the source, and the salvation of Zion."
Not true. If this is the route that all Neo's predecessors have taken, then the Architect has just explained that Zion is always destroyed. Returning to the source will not save Zion; it will merely allow Neo to rebuild it. I would hardly call it "salvation" if everybody is killed and he has to repopulate it with 23 people plus himself.
Then: "The door to the left leads back to the matrix, to her, and to the end of your species."
Again, not true. There is no indication what will happen if Neo doesn't immediately return to the source. The Matrix will presumably keep running, and the people attached to the Matrix will presumably stay alive. There's no reason to think otherwise. I think it's safe to assume that Zion is destroyed, since Neo doesn't do anything to stop it and their situation is otherwise pretty hopeless. Unless, of course, Neo can return to Zion soon enough and use his new special outside-the-Matrix superpowers to stop those damn machines from digging. Or maybe Agent Smith will have something to do with it. After all we never really found out what Agent Smith's "purpose" is except we think he wants to become human (cutting himself to feel pain). If this story follows the pattern of every Frankenstein story, Agent Smith's "purpose" is to kill his creator (the Matrix, and the Architect in particular). There is of course the school of thought that says that Zion was actually part of the Matrix all along, a matrix-within-the-Matrix, and that "freedom" was merely part of the system of control. But whatever.
Along with a lot of other things, the Architect's speech sat uneasily with me, as did Neo's final "choice." Now I know why. If you forget briefly how bad the movie otherwise was, this was a cheap plot shortcut that simply doesn't make sense on the face of it.
I couldn't figure out what the hell happened in the final battle. Was Zion destroyed or not? This blogger tries to answer the question. You have to highlight the text with your cursor to read it.
All in all, I found The Matrix Reloaded to be a lot like a mediocre second-season Twin Peaks episode.