As far as the alternate timeline goes, and I know people have said this before, Emet-selch is still alive in that timeline. I kind of wonder if he caught wind of the Ironworks and Exarch's plan and stowed away and is the shoebill sometimes. Seems too simple though, to be something unpredictable.

I like the Atomos idea, but considering Atomos is voidsent rather than an almost deity like creature in XIV, I don't think that would be likely.

There's also an Echo vision the WoL has right at the end as the GC leaders are all speeching it up and celebrating victory over Ultima Weapon/XIVth legion where he sees Hydaelyn and the Shards as crystals of darkness. I wonder if or how that will ever play into anything.