As we all know, Archaeotania is a concept created by a frightened Ancient during the Final Days. It was captured and brought to Amaurot's Akadaemia Anyder to be studied and analyzed, but it broke free and wrought havoc to the city.
For all we know, Archaeotania itself is simply a FFV reference. It uses FFV's Twintania's abilities and its horns can be used to buy a Tinker's Bell minion, like the Tinklebell weapon in FFV.
Still, when looking at it through an exclusive FFXIV point of view, Archaeotania becomes really confusing. I have no reason to think the Archaeotania we fight is any different from the original Archaeotania; that Emet-Selch's power failed when he was making this part of his illusionary Amaurot.
Archaeotania is draconic. It uses Bahamut abilities like Gigaflare and Megaflare. It summons "Ancient Aevis" adds, who use Alte Roite -- in FFV called Jura Aevis -- models; both aevises and alte roites being humans who can turn into dragonlike beings.
The implications would be that the pretty innocent 1) as per Archaeotania being born of fear, at least one Ancient knew what dragons were and feared them; and the more scandalous 2) as per the presence of the Ancient Aevis adds, there were Ancients that could turn into dragonlike beings for some reason. It couldn't be that there were dragons on the Ancients' planet because there are no sundered dragons, so... why?
(Archaeotania also uses other Primal abilities like Leviathan's Tidal Wave, but as it was born millenia before primals, I don't think there's a direct link to them other than "the legend of Archaeotania influenced minds and thus this reminiscence resulted in primal abilities when they were summoned".)
I find it hard to believe the dev team would just throw something big and lore-bending like that -- featuring not only a FATE Chain for a World FATE but also the Akadaemia Anyder dungeon and a big player in the fall of Amaurot -- for it to be only a FFV reference and nothing more, being actually unrelated, "we know it makes no sense, don't pay attention to that" style. They went out of their way to make sure Seiryu, a dragon in every incarnation, not a dragon because it would mess with part of the lore that says every dragon is a descendant of Midgardsormr. Every reference like Gilgamesh or Eureka is sewn into XIV lore, never being "just a reference". Even Omega's creations are justified as being local legends or things from other shards. People could find links in lore to the smallest things like Azem's grapes and the Temple of Qarn's grapes... so what's up with Archaeotania?
If Archaeotania is truly a draconic being in a pre-Sundering time, what could that imply? With dragons being relevant again in 6.0, maybe we're in for a ride or something I guess?