Can I start off by saying that overall, I think the team did a great job in tying up the story into a satisfying conclusion. I definitely enjoyed my ride throughout the game and commend the team for the work that they put into this expansion and the this whole saga in general. However, that is not to say there aren't any issues with the story.
I will be talking about spoilers in the Endwalker and Shadowbringer expansions as this talks about an A LOT of important aspects introduced in the later half of the Endwalker story. Do not read below if you don't want to be spoiled.
TLDR: I think the introduction and application of dynamis was lacking.
The main issue I want to focus on is the introduction of dynamis into the story. Since the beginning of Realm Reborn (maybe even in 1.0, I wasn't there for that, please correct me if I'm wrong), aether has always been the main source of energy and power for all life in the universe of FFXIV. From the magics and techniques used in our combat jobs to the creation magics employed by the ancient godlike Ascians. To introduce dynamis, a completely different power source so late into the story of this saga that has been told through multiple expansions feels like it was pulled out of a hat to move the story forward. As if they needed to find an excuse why Meteion and her sisters were the ultimate big bad and this was all they could come up with, that aether doesn't work on them.
Now, I would be inclined to believe in this concept of dynamis, had the authors left hints throughout the expansions (not a lot, but maybe 1 or 2 here and there throughout the saga), that alluded to this secondary power source that apparently encapsulate more than half of the universe. The only hint I remember is in the 5.0 story of Shadowbringers, when we're in the Amaurot dungeon watching Ascians create abominations due to the dynamis infused into their creations by Meteion. I cannot think of any other time where this application of dynamis is alluded to by any particular event, person, or thing. Right now, I'm just not convinced that the writers of this story properly implemented this concept of dynamis.
BUT, I'd love to be proven wrong and if anybody here thinks that there has been any such events I would love to discuss about it in this thread.