Finally, some good food.
I think the first place they went wrong was in their original idea that seems to have existed before the writing actually started on EW that there should be a surprise boss at the end that isn't Zodiark or Hydaelyn. They could certainly have kept this in and have a good story, but I think a lot of the mess was when they introduced this and how they attempted to reconcile it with the story that was already given to us in Shadowbringers.
Problem number 2 is part of problem number 1 and it's that Oda apparently really likes space and that he and Ishikawa wanted a space zone, which required a reason to go to space, specifically led to Ultima Thule and not the moon according to interview, and made a further mess of things.
Problem number 3 is time. While the 6.0 MSQ is longer than the other x.0 MSQs, it has too much story to tell, not enough time to tell it, and doesn't make good use of the time and space it has to tell it. I feel like at least half of Labyrinthos and all of the Moon were wasted both in the narrative and in their use of the zones. Ultima Thule suffers from 6th zone syndrome where the last zone in an expansion ends up being mostly about the spectacle and a mad dash to the end. Needing to wrap up every last loose plot thread didn't help either.
Problem number 4 is Shadowbringers. Yoshi-P admitted that too much was revealed to keep milking the plot a few more years and that they had to end it in 1 expansion. The other problem from Shadowbringers is its success and the need to follow ShB. Emet-Selch ended up becoming a fan favorite due to reasons covered in another thread and I feel like the writers felt that since Venat had been here since ARR and was more important to the story, she also had to be a very complex character with moral dilemmas to copy his success.
And problem number 5 is the fact that this is an MMO and the narrative isn't organically grown. Summing up all of my points above, the story had to fit into a box where there is an established trial, dungeon, zone, or half of a zone at specific levels and they're set in their ways and won't budge the established outline to satisfy the narrative. So they have to build the story around the framework of the game instead of allowing it to tell its own story as a book would. The whole ending wasn't planned from the very beginning either and Ancients didn't even exist in their heads in ARR. Ascians were just "doing bad things" and praying to their one and only dark god to plunge the world into darkness until they could figure out what to do and build the story as it was live. Then they had to take everything random they're adding in as well as unnecessary flourishes to characters or backstory to make things more "interesting" and you get what we got.
This is why I am more forgiving of a story's intent and less interested in pulling the plot holes apart when it comes to this instead of a book or a movie. They're completely different mediums that should not be compared on equal grounds.
They could very well have kept the whole "keening from inside the planet" and have us chase down some "original blasphemy" inside the planet but they needed a reason to go to outer space. Which probably led to the final boss thing being a creation gone rogue that went to space, so they needed a reason why it would do that. But the reason is very complex so we needed a whole fanservice zone in the Ancient's time to show what happened. But because we do the whole thing with Emet, Hythlodeus, and Venat, we need a reason for Emet to not remember us. Then we get into the whole thing of memory wiping, but not Venat for some reason, and then the plot holes start forming. Her characterization then becomes more unbalanced against what we already know about, expect, and are supposed to sympathize with her.
Difficult to reconcile concepts like Dynamis and the wonky Elpis time travel story ended up getting made just to satisfy the unwieldy plot and don't feel like they're naturally introduced well enough to prepare us for them unless you count the color changing elpis flower.
I think the simplest change for the better would have everything remain the same up until the end of Elpis despite how much I feel let down by the moon. Even if Venat also lost her memory, enough had already been gained to continue the story without as many plot holes. We found the cause of the Final Days and it would've tied off any time travel paradoxes. Hydaelyn could very well have recovered her memories as Venat after taking up her role sitting in the Lifestream due to some magic yadda yadda and become a tragic figure that way. The whole Sundering thing could have remained a tragic accident due to strong wills and a side of tempering.
Some stale food.
This same discussion happened back in 6.1 and like I said back then, how is this any different than us generating a Carbuncle and sending it off into battle back when they could get targeted by enemies or tank for us? Carbuncle and the Nixie are both similar familiars that are nothing more than pure aether magicked from inanimate objects (a gem or water in each case) and given form to do a task. Poroggos are actual frogs who were uplifted and given intelligence and everything about their story is cruel and none of it is played as something sympathetic to their original masters.
Y'shtola then dismisses her Nixie as one would to a Carbuncle. Does that mean that every time I de-summon my Carbuncle I'm committing acts of cruel violence to a familiar? No.