Here is my take on some things, and a brief history lesson of Eorzea.
Okay so I don't 100% think that the Allagans are gone. On the simple side of my thinking, the last few Allagans are in fact the Garleans. On my more complexed side of thinking, the Allagans are really; wait for it.... in space! The Allagan Empire constructed the Royal Allagan Sunway and Starway in what is present day Thanalan. They had to have advanced spaceships based on this and everything else we know. A part of the Allagan Empire, be it most likely a small portion, could very well have escaped the end of the Third Astral Era on spaceships and be on the moon somewhere or something.
As for the Primals, we know that the Elder Primal Midgarsormr was protecting the "Seal of Silvertear Falls". The seal was most likely made by the Allagans to deal with all the lesser Primals, and based on what we've seen on the Binding Coil (Most notably the Dragon Twintania, and the other dragons with it in Turn 5), we can safely bet that Midgarsormr was defending the seal because it was under the control of the Allagans. The Garlean Empires armada posed enough of a threat that Midgarsormr was awoken to defend the seal. I don't think that killing Midgarsormr is what broke the seal though, but...
The Elder Primal Bahamut was most likely the reason behind the Second Astral Era ending, and the Third Umbral Era ended most likely due to the Allagan sealing away Bahamut. Now weather they sealed Bahamut up, then made Dalamud or if Dalamud is what they sealed him away in is unclear. But my guess is that they sealed Bahamut away, and then built Dalamud. This also means that the Third Umbral Era must have lasted a really long time since the technology to seal him away would have taken a long time to develop; not to mention the fact that it would take an extremely long time just to get technologically advanced enough just to be able to develop that kinda technology. The Weapons (Ultima and soon to be Omega[maybe], and maybe more models) were most likely used to fight Bahamut so they could seal him away.
Dalamud, which was in space between the world and the moon, is nothing more then just one great big power plant for the Allagan Empire. Crystal Tower, for whatever reason, was drawing power from Dalamud. Most likely, but probably not (yet maybe), Dalamud transferred power to other Allagan places that are yet unknown to us. Since Crystal Tower is most likely the only 100% in tact Allagan installation (or whatever you wanna call it), it is mostly the only thing that Dalamud had to send power to.
Huh, is it me, or do the Allagans seem to have a knack for using dragons to do their bidding in one form or another?
I have way way WAY more, but I'll leave it at that tid bit for now!

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