The clones of Emet.

[Rosenstrauch]

Actually, that wasn't retconned, it has been linked up. The crystals weren't used to possess people, although it was a fair mistake for the Scions to make in-universe, because what they actually do is use them to travel between their 'home base' in the void and the Source and its shards. Thancred snagging one of Lahabrea's crystals didn't directly cause him to get possessed, it just gave Lahabrea a very easy target when he'd otherwise have REALLY had to look to find someone as well-positioned as Thancred.

That sounds exactly like a retcon to me. But okay, fair enough.

And as for the Imperial line of succession... well, remember that the title of Emperor was held by Emet-Selch as Solus right up until his death. And he deliberately didn't name an heir, because he wanted Garlemald to freak out and pull knives on each other. We know that the war of succession was between Varis and Titus--although Titus was named later. We know NOTHING about Titus, including his relationship with Nerva, but she was mostly considered the main competition to Zenos in the second war of succession not really because of blood rite, but because Zenos is nutsbar crazy and she is, presumably, not.

I'm not sure you understand what I'm talking about when I say "Nerva's existence is a plot hole", so I'll elaborate. Nerva was first introduced in patch 5.2/5.25 via dialogue between Menenius and Lyon after the events of Castrum Lacus Litore. Specifically, Nerva, Legatus of the IIIrd Legion, had ordered Gabranth and the IVth Legion to return to Garlemald. Gabranth had refused, and Lyon had this to say on the matter:

I thought as much. Not that it matters. Nerva is just like his father Titus, weak and a coward. Unfit to give orders, let alone lead a nation.

Thus, from his very introduction into the story, Nerva was established to be the son of Titus Galvus. The problem with this comes from the short story In Darkness Blooms the Lily, where it's established that one of the reasons Varis had stronger backing for the throne in the wake of Solus's death is because he had a ready heir in the form of Zenos. By contrast, there was no one who could succeed Titus if he took the throne and then died.

It's a minor plot hole at best, and one that could be easily filled in. I bring it up entirely because it hasn't been filled and from the look of things it might never be, as the IIIrd Legion are now the Telophoroi—tempered thralls in service to Fandaniel and Zenos's whatever the heck they're doing.

https://na.finalfantasyxiv.com/lodes.../sidestory_05/ - The story in question