So I just beat this last weekend and after letting everything settle in my head for a week this is what I've come up with.
1: The entire story, start to "Wake Up" is a flashback. That's why Vanille narrates from the past tense - it has already happened to her. The characters having turned to Cyrstal are reliving the events. This is why the backstory is fragmented instead of linear(1), the characters are replaying it to the audience. This also explains why Vanille and Fang are with the party once you save after 'beating' Orphan, though the extended play save can also be explained by developers being lazy with new game plus. Personally, I like the flashback scenario. It makes the the fact that you are being 'told' the story much more palatable.
2: Ragnarok - Here's where the Analects provide back story and also confuse things a bit.
During the War of Transgression Fang became Ragnarok and broke cocoon open. A goddess named Lindzei saw this and turned Fang and Vanille to crystal. (Analect 4). This is also the same goddess that created Cocoon. We know that the people of Gran Pulse knew the name barthendalus. It's in the text of the marker at the end of chapter 11. So who's this other bitc, and if she loves Cocoon so much why does she let a sociopolitical demigod keep running the place?
There's honestly not enough about Linzei to be sure of anything. Maybe Versus will explain it more - the point is that she is mentioned separate from Gran Pulse in the same manner - a creator who abandoned her people. Maybe she is Barthendalus as the special edition guide suggests - but then we have to again wonder what stopped Fang and Vanile from destroying Cocoon the first time? This is the biggest plot hole in the game and I have a hunch that Versus or Agito will resolve it.
3: My take on the end after the death of orphan is this. Their focus complete (Orphans death means cocoon will be destroyed) they all start to turn to Cyrstal. By becoming Ragnarok Fang and Vanille avoid this, create the pillar to hold cocoon and then transform back. Their transformation into crystal expands to the matter around them, 'saving' the world. The reason that the other 4 brands are gone is because the original Fal'Cie is dead and cannot sustain their crystal form. Fang and Vanille never revealed which Fal'Cie branded them, and since Orphan only powered the Cocoon Fal'Cie their stasis remains.
1: The game is linear. The backstory itself from Day 1 to 13 is told in fragments.
I'm going to bed, i'll reread that in the morning and correct any silliness. My biggest "wow" moment was realizing that the whole game was a flash back. It allows for sillyness like Dysley usingas much as he did.
XI Wiki

as much as he did.

