A new headcanon just appeared in my mind...Azem made the Shoebill originally as a case of "What if I created a creature and have it act like Emet-Selch?" The shoebill follows the WoL because it's just as fascinated with them as Emet is. :p
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For that matter, has the ambystoma made any sneaky appearances post 6.0?
The shoebill seemed to have at least one cameo per patch up through 5.3, but I haven't noticed the former since Ultima Thule.
The faefolk were always a...weird case to me given that they seem to be wholly absent from the Source.
They're believed to be the souls of children who somehow didn't pass on to the Lifestream and instead lingered in a new shape, but that's a strange exception to the usual permanence of death given that even ghosts are hand-waved as not literally being souls of the deceased but rather more akin to arcane constructs created by the lingering sentiments of those who've already passed on proper.
I feel like they might not be absent so much as decentralized. They don't have a single specific seat of power to congregate in, so they're much more spread out, and probably doing much smaller things without the safety net of an entire kingdom to support them.
This is definitely the sort of thing I'd expect to get sorted out by the Encyclopedia Eorzea 3, though, and probably isn't important enough to get discussion outside of that.
Just a word of warning. We visited one facility on Etheirys. While one might be able to draw conclusions about some of the creatures we have encountered from that visit, I doubt that the facility held samples of every living creature in the world.
I don't remember seeing Au Ra, Miqo'te or any of the other peoples we've encountered during our visit. Just a lot of 12 foot tall Hyur.
They seem to be doubling down on the angle that the present-day races are largely descendants of the Ancients who were born of the imperfections they bore post-Sundering.
The fact that Hyur are the only race who don't get immediately dismissed as some manner of familiar due to quirks small or otherwise seems to support that there was only a single race of man back then.
I feel like Myths of Realm is the most likely place we'd get an explicit clarification behind that in-game if anywhere, though.
When going through Elpis, I know that hyur and elezen get it mentioned that we look pretty much exactly like Azem, while the more unusual races like au ra, miqo'te and hrothgar don't get that, instead leaning more on the similar aether. We're treated as familiars no matter what, though.
I'm not sure what roegadyn and lalafel get; realistically I could see those two going either way on that. Hyur and elezen getting that treatment makes complete sense, though, since the Ancients have a structure of 'elezen frame, hyur head' that a lot of the more 'generic' Garleans also get.
Lalafells and Roegadyn get called out more then the other races since even in the initial Elpis cutscene where we get "fixed" by Emet-Selch, Hythlodaeus will accuse him of being lazy/overdoing it due to the size discrepancy (Though I think the latter might apply to any of the particularly tall race/gender combos).