I think a lot of people would do well to remember that FFXIV isn't written in the same way as any other FF game but XI, and hasn't been since, if we're going to be completely honest, somewhere in 2010. Writing for a live service game requires a fundamentally different approach that's more akin to a long-running comic book or manga than anything else; because you can't perfectly predict where the future will go, and you can't easily edit what's already out there, a key part of the writing involves rewiring the parts of the story that were already there to serve the story that you're telling now. The fact that they're doing so isn't a failing of anything or anyone, because a story outline that exists across ten years and multiple writers is inevitably going to change, be refined, and be influenced by newer (and you would hope largely better) ideas.
I think the way that XIV did it with the Zodiark and Hydaelyn story especially was extremely smart, because they used it to accentuate the parts of characters that were needed for the story to work: namely, their flaws. Hydaelyn's info was unreliable because she's been hiding uncomfortable truths and acts for twelve thousand years for a greater good that she can only hope happens. The Scions' info wasn't always accurate because a core part of their story has always been to learn, to become better people with a greater understanding of others. And the Ascians went through more transformations of writer's intent than we can probably count, as they transformed from megalomaniacal monsters to, essentially, horribly broken people trying to bring back an idyllic past that they didn't truly understand.
Could you possibly write a form of FFXIV's story where all of the 'final forms' of those characters were present from the start? Yeah, probably. But the nature of a game like XIV is that they just can't edit those earlier chapters, so those refinements instead have to be written to work with those earlier ideas. And I think a crucial element of what makes all of it work is that they respect what came before, even as they reframe it: Hydaelyn's previous statements are never thrown in the dirt and rejected, even as they're shown to be lies, partially because they're shown to have elements of the truth. I actually think the best example of this is Lahabrea; it would've been so easy to just dismiss him as a completely unhinged raving lunatic who's lost touch with everything just so that we could easily dismiss his whole rant, and other writers might well have done that. But instead they went to great lengths to show how he got to that point, and to give him elements of truth that we can trace.
All that is to say, I hardly think that being able to recognize when something's changed is a flaw of anything. It just means that you can recognize how the game is written.