First of all, they outright stated that the original intention of the two queens was to allow the two worlds to merge safely, to COMBINE them so that neither had to be destroyed in the inevitable draw toward each other. After all, those two universes were originally OUR world, that got unmade/re-written/choose your interpreation by Klaus' experiment. It was unnaturally sucked apart into different realities and those realities were being drawn back into a whole. The game tells you that it is irresistable and they can't help it. So even if they got separated, they'll just start to be drawn together again! The goal of Origin was to let them become one without the destruction of either. For the realities to merge rather than destroy each other.
But, at the end, Noah is somehow given a choice, right? So the reason the worlds separate is the main party's choice based on their total experiences thus far? But why is separating a good thing? Wouldn't the original plan have been better to follow?
Btw, at the VERY END, I finally loved Riku, lol. The adorably tear-spewing MA-NA-NAAAAAA! Made me laugh at a moment when I really WANTED a laugh.
He was finally acting like Nopon rather than Darth Vader in a Furby's body.
Dang, thought about that so hard, I've forgotten the second thing I was particularly confused about. There were all kinds of small things, such as how long it's been since XC1 and XC2 (which were happening concurrently, as the end of XC2 revealed) Oh wait, no...now I rememeber. Okay, so TWO worlds. BOTH were kind of erased by Moebius snatching control of Origin. Bits of them were forced together, geographically...and so were all the people. The souls were used like raw material, to make a bunch of new souls?? Is that how the people of Aionios were created? I'm going to assume that Nia and Melia were preserved as they were by being inside Origin or something...I can't spare the the brainage to wonder how ONLY they came through unscathed when the plan went wrong.
I assume that Moebius had a hand in it. He used the souls to create people as they were, to, what? Be fuel to continue running Origin as a machine that forcefully held the two universes together? Some broke free thanks to the creation of Ouroborous, and those who broke free basically were able to return to being normal humans in that they then had normal human lifespan. In at least one cycle, Noah and Mio themselves were free and had a kid. I guess they were two of the 6 founders of The City? So a lot of the city folk are genetically their descendants. (Though mentally, in terms of memory and life experiences, they get recreated anew and are new people each cycle.) Lanz, Sena, Eunie and Taion appear to be people they met only in this cycle...they're not the other 4 of the 6, as far as I was able to glean.
Just how long had Aionios been existing? Nia and Melia are about the same age, since both were considerably older than their very young looks in their own games, and both had very long lifespans (though technically, only Nia is actually immortal. Melia as far as I can tell shouldn't live more than a thousand years. Ages were known in XC1, you could even see them on the affinity chart, so, seems like the lifespan of a High Entia was around 400 years at the most, though maybe she gets a bonus from being royal blood or something. (But I don't think so, because Sorean, her father the emperor and a pure-blooded royal, was biologically quite old and he was only 320. Kallian still looked about 24-30, and he was 150.)
Also, uh...how did separating the worlds work? Did Origin recreate everything that existed the moment before it created the whole mess that is Aionios? Poppy has reason to still exist in the XC2 universe, but everyone else would be new people...no more Rex, unless sharing Pyra's soul made him immortal. But what about the people of this third reality? They don't actually belong anywhere, do they? Or are the Kevesi the people of XC1's later universe and the Agnians the people of XC2's later universe? I thought it was more like the poeple were the people of both worlds, smushed together weirdly like the landscape, so they're people of an entirely different, third world that no longer exists. I AM CONFUSED.
Why did Nia nod at Riku? There were several hints in the game that Nopon were actually key to everything, or in-the-know about it, but they didn't resolve that, did they? Certainly Nopon are special, existing in every universe, even X, and the Sage in XC1 is listed as 9,999 years old, which is basically like stamping an unknown or infinity sign on him. He's eternal, without beginning or end, or something. Maybe he's the freaking Zohar after which Monolith Software is named, lol. (The Zohar is the 'monolith' they refer to. AKA: The Conduit. The otherworldly thing found in Africa of our world that Klaus used to power up that stupid experiment, storing it up on space station Rhadamanthus after it was found, to isolate it safely, I guess. Dang, this is a weird series!)
So much of the entire Xenoblade saga is never actually explained and we're left cobbling together explanations from what bits we know for sure and using our imagination to patch the gaps.