A lot of repeating, this is what I wrote up immediately after finishing the MSQ so I can look back in 3.2 and be mad at myself for being so wrong/stupid.
I figure Yda and Papalymo are in Ala Mhigo, helping the Resistance. (The NPCs in Rising Stones seem to hint toward this as well-- they mention believing Ala Mhigan refugees in Ul'dah helped spirit the Scions away.)
Elidibus and Urianger's book is another nod to XII. "Gerun" was the leader of the Occuria. The Occuria, of course, created the Espers in XII -- including Zodiark.
Confusingly, the book is in the Forbidden wing of Gubal, which means the Sharlayans found it dangerous.
The most likely scenario is the book contains the "true history" of the beginning of the Hydaelyn--more than likely a very different tale than we're presented with the Age of Gods.
I suspect Matoya's Crystal Eye is a Crystal of Light from the First Umbral Era, since she's a nod to FF1 (which would make it extremely powerful).
Krile's speech to Matoya was awful. Hydaelyn is the "Light" and she received a gift (the Echo) from "the Light"-- a blessing of Light. It's troublesome wording but I believe her not to be possessed of the Blessing. She has a blessing of Light, not a Blessing of Light. Rather irksome nonetheless. The journal says "not only does she possess the Echo, but has availed herself of the blessing of Light's protection." So I eat crow here; she has both.
Thancred's one good eye has been whitened like Y'shtola's. I wonder if this is indicative of a similar blindness or just a "hint that not is all as it was." So does he see aether too or is his newfound Garleanhood the only side effect.
Edmont is savage tho, poor Artoirel. Right in the front of everyone lauds his bastard son above all else compares the Lord Commander to be a favorite son in front of his own kin. It looks like both of Haurchefant's brothers will get fleshed out, which is rather nice. The younger doesn't particularly seem to be on board with everything that's happening now...
We also never saw what happened to the priest who tossed the girl off the building. I hope the Scholasticate quests delve more into this.
Where the hells is Nidhogg off to? I'm expecting Azys Lla.
The return of Alisaie is the single most hype thing from this patch and if you disagree you are wrong.
Also I don't remember if it's changed since 3.0, but Urianger is no longer idly reading in the Waking Sands. I mean he's there, but it's weird to see him without his nose in a book.