I think we just need to accept that the writers were never the brilliant storytellers they were percieved to be and just made a good story (albiet still flawed) by accident. Watching how the story has unfolded, listening to various interviews where they talk about the story and attempt to explain certain things, it becomes clear they don't really know what they're doing, barely understand their own story even. Listening to story interviews, there's a lot of "ums" and "uhs" and "I think" and "you know maybe....", they don't seem to really be certain about their own story. They're not just sitting down and being like "alright so this is why this happened" with absolute crystal clear clarity and consistency with what they've said before.

This is a lot like George Lucas and Star Wars, where everyone loved the OT and thought Lucas a genius, then the prequels happened, people listening to his takes on his own story through interviews and it became painfully clear he had no idea what the fuck he was even talking about, and that the OT was good was only by pure accident.

Also, much like George Lucas, FFXIV's story cannot entirely be credited to the current writing team. Like how Lucas wasn't actually responsible for as much of the OT as was originally believed, much of the good writing credit FFXIV get's cannot really be attributed to Ishikawa or Yoshi, but various different writers that have been involved since 1.0 in and out of the writing team and are probably more responsible for elements of the story/worldbuilding that we enjoyed than the people ACTUALLY in charge of the story and currently getting all the credit.