Interesting that the Sin Eaters have been a problem for a century! That implies to me that the Warriors of Darkness were ALSO from a hundred years ago. They claimed responsibility for causing the Flood of Light, and the Sin Eaters presumably started to appear AFTER the Flood began. That implies that the WoD's did all their Darkness crushing way back then.
Of course, if the Flood has been going on for a century, it's interesting that this is the first we've heard of it. The Asicans must have known. Is it possible that Hydaelyn DIDN'T know, even before she was depowered saving us from Ultima? Could the Shards be hidden from her view? She seemed to be eager to go help once the WoD's spilled their sob story, so it would be curious if she's known all along and didn't do anything previously.
As for Hy and Zo being Primals, I don't really doubt it, but think it's more likely they're Primal-like beings rather than exactly like the Primals we know. As others have pointed out, they don't (seem to) drain Aether, and we seem to have an awful lot of free will if we've supposedly been tempered by Hy. (Of course, our free will could be Hy's command to us. Reminds me of the episode of Gargoyles where Demona succeeded in turning Goliath into a mind-controlled puppet who obeyed every command. Elisa's command to him? "I order you to act for the rest of your life exactly as you would if you were not under a spell.") I've long had the suspicion that the Primals the Ascians teach people to summon aren't the only possible kind of Primal - that the Primals were deliberately constructed to be harmful, chaotic, and Aether-draining becuase that served the Ascians' purposes. Hy and Zo could be "true Primals", and free of the problems the Ascians deliberately included in their summoning process.
This kind of alternate timeline stuff works fine when you have a multiverse with nigh-infinite variations. Unfortunately, in this situation we have only fourteen variations. It's the whole infinite monkeys thing. With an infinite number of monkeys tapping random keys, one of them is bound to write the Complete Works of Shakespeare just by random chance. Now, try it with fourteen monkeys, and see how likely it is to happen. With infinite universes, sure there might be a sci-fi version of you, a fantasy elf version of you, etc, etc. But in just fourteen universes? Very unlikely.
As you say, it is not impossible. However, as RenewalXVII says, it's amazingly improbable. For events on two worlds which, while they might have started as identical, have done their own thing for twelve thousand years, to somehow assemble the same set of genes (or whatever this fantasy world has instead of genes) to create two copies of the same individual? Absolutely ludicrous to the point of shattering suspension of disbelief.
Anyway, the way the scene with the two Minfilias played out looked a lot to me like they were about to merge together. I'm guessing that Minifilia is a part of Minfilia that split off of the Emissary to act as an incarnate presence on the world, and when her task is done she will rejoin with her. Why such a presence was needed, remains to be seen...
Sorry, couldn't hear you over the sound of turning the whole planet into a magic circle to shoot you into another galaxy so hard you both explode.
And Sephiroth thought he was so cool with his attack animations! Well, la dee frikkin' dah!