These are my personal grievances with the story. Emphasis on "personal" since I understand why some people would enjoy it and I recognize the appeal, but it just didn't resonate well with me:
Sudden plot elements: Hermes, Meteion and Dynamis were just too abruptly introduced in the story. Yes, we've heard of the seat of Fandaniel and we knew of "the sound" but the thread of correlation was too thin between what the player knew and what was introduced. I think it's important for stories to have a build-up and continuity of some degree, that makes you speculate about the elements and where they might go from there, but if you drop new, all-encompasing elements all of a sudden, it's hard to keep me invested because at any moment you could just drop another one and leave me in the dark again. I ended up caring very little about Hermes and Meteion which took away from the whole experience since they're central aspects of it.
No, I wasn't expecting Zodiark to be the "big bad", but I think there were other possible venues of storytelling they could've chosen using pre-existing elements instead of adding entirely new ones right at the relative end of the story, in true Final Fantasy fashion. I wouldn't have enjoyed FFVI as much as I did if Kefka was only introduced at the Floating Continent when he's about to tap into the Warring Triad's power. Even the infamous Yu Yevon from FFX had some modicum of foreshadow and previous exposition.
You could retroactively apply Dynamis to previously established lore (such as the Omega raid or Limit Break), since it's such an abstract and vague concept, but that's not good world building in my opinion. Who knows now what's Dynamis and what isn't? Will they even bother to articulate it with future stories and, if they do, will they at least give it a more concrete explanation and modus operandi, or will it be relegated to a very anime-esque plot device for when the WoL is in trouble?
Time travel: Time travel often does more harm than good in the story. I'm not saying you can't have an interesting story with time travel, but it does require a neatly packed frame since the chances of contradiction and plot holes are enormous.
EW not only did time travel, but they decided to do the closed loop variant which is, in my opinion, the most flawed one. The whole "who comes first..." scenario just feels like a cheap excuse to not give proper causality to the events presented: it expects you to just accept that it is what it is and to move on. No sense of wonder as you unfold the reasons, no theorizing about the contrivances involved, no speculating about its widespread unknown impacts and variables, nothing.
Theme: Nihilism is, quite frankly and very personally speaking, a very boring theme. For every german philosopher and indian monk claiming that there is no meaning to human existence, you have millions of people giving meaning to their own lives, be it through faith, love, ego, personal goals, legacy, values or even just hedonism.
I think it works well when it's tied to the development of a character with relatable traits, surrounded by goals, flaws and situations that make said character adopt a very personal, subjective type of nihilism, shaped by their own trials of life. Caius in FFXIII-2 comes to mind.
Suffice to say, Meteion is quite the opposite... although it makes sense considering what she is. Her take on nihilism was extremely shallow and juvenile and it kind of dragged the whole writing with it. At some point when it was just the WoL, the twins and Meteion in Ultima Thule, the dialogue was almost reduced to "My hope is stronger than your despair!" and "No! My despair is greater!". This is the type of writing I expect from something like Danganronpa - and I quite enjoy Danganronpa, but for the comedy, not because I take the writing seriously.
I never understood why some writers present hope and despair as if they were some kind of hidden yet concrete power that you declare to others. Emotions are more complex than that, specially when interacting with the emotions of other people. I think both themes are better presented when they're subtle and preferably not even mentioned: they're emotions and they work better setting an atmosphere. You could feel the despair and the misery of those garleans in the subway refuge, or in Quintius' melancholy: the story and its chracters don't need to spell it for me.
Fantasy vs Reality: Sometimes it feels like the writing is not sure if it's based on reality, based on fantasy or the latter constructed upon the former.
I think it was mentioned in this thread before, but the Ea is arguably the biggest example: in this universe where the equivalent of matter is well known and even interactable, where people have created underground suns, sent ships to the edge of the cosmos - which is 60% something made of "emotion power" - and all sorts of rules of physics are nonchalantly broken by fantasy elements, why is the game telling me that suddenly thermodynamics and the entropy of the universe is a big deal?
I could stretch the point to the Ancients. Of course they have a different view of death than I do: they're virtually immortal beings with demiurge-like powers, living in an enlightened society articulated by social dialectics and communitary values and - more importantly - with a clear understanding of the cycle of life and death. Me, the poster, have some decades of life ahead of me, have no idea what happens after I die and am surrounded by a world filled with animosity, strife etc. The game expecting me to so readily apply my own sense of life morality to a world so detached of my own feels forced. Perspective is everything.
In fact, some of the reasonings for the despair of certain worlds (like the Ra-La one) seemed to completely disregard how complex people tend to be, specially when on the verge of destruction and how we always aim to adapt and preserve life. But then again, those worlds may have been under the Endsinger's influence to begin with so no point in commenting further.
Ultima Thule: I loved the zone's atmosphere, specially the Ea part which really sold the eerie alien aspect. The music (the instrumental one) was also on point. Other than that, unfortunately, I feel it was one of the weakest parts of the expansion.
Admittedly, that's mostly because of the abovementioned points, but the zone just sank my expectations further. I can understand when people say the scions' "sacrifice" was just for the message, but that doesn't change my perception that the entire thing was a completely pointless, overly sappy waste of time.
The moment Thancred "died" and the characters were just "okay, moving on", that was already a sign. When Estinien was "dying", the first thing I thought was: "Oh, it's gonna be one of those moments" that have been done countless times in other japanese RPGs and animes. Just because something was done before, doesn't mean it's bad, but Ultima Thule did it in such a formulaic, non-impactful way that whatever immersion I had was just replaced by "Alright, here's zone 2, who's next to make the speech and disappear so we can move on?" When the writing becomes this predictable, it becomes hard to create immersion to begin with. I feel they could've just kept the scions there the whole time, interacting with the different alien races and it would've probably been better.
And before someone says it: I don't think killing characters for the sake of emotional impact is good either. That said, this expansion was advertised as an apocalyptic moment. There is a limit of how many random NPCs you can kill in the most tragic ways before it stops being impactful because the main cast just seems to be immune to it. You don't have to kill the scions, but surely you can leave scars - both literally and figuratively - on them: it's a sign of development and of the stakes the story is trying to present.
Why did a banquet in ARR leave a bigger impact on the scions than the actual end of the world? Also, notice how the WoL's dialogue became influenced by Haurchefant and even Emet-Selch: because those characters left a legacy after death that shaped the protagonist's view. Death doesn't need to happen everytime, but it can improve a narrative and I feel EW had some great opportunities to use it.
With that said, some people saw EW as more of a conclusion to those characters, since they were already completely developed by the end of SHB, and that's fair, but if that's the case, I feel it was a very boring conclusion.
Other points I could mention (plot conveniences, the whole Venat thing) have been said countless times, so I won't extend this wall of text. Apologizes if any of this sounds condescending or overly picky as it was not my intention: if anything, I'm criticizing EW the way I am because of how much I appreciate this game's story and lore.