I've been mulling over my thoughts because my initial reaction to EW was not positive. I needed to sift through the negativity and disappointment to write something coherent. :P This turned out to be a lot longer than I thought, so I'll have to split it up into multiple replies. Assume full MSQ spoilers. 1/3
Inconsistencies:
I lost track of how many times I was given pause because the narrative in EW didn't match what had been presented in previous content. I hesitate to say "retcon" because I don't want to have to go through and make a bullet list of them for debate, but that was my first thought every time. I know it was the same writer, but it felt like either the story had been handed off to someone else for a different interpretation or they discarded the path they were charting in ShB which led to lore rewrites and dropped plot points.
Zodiark:
Learning that Zodiark in the 'Hydaelyn & Zodiark' saga was little more than Gundam suit was disappointing. A major 'character' who had been name dropped since ARR, who was either the greatest threat to life or the savior of it, had no presence at all. The only argument I've seen against this is that Elidibus was Zodiark, but I didn't find that satisfactory since we'd already dealt with him in ShB. I also took issue with his model. It may have looked cool, but such a monstrous looking being didn't fit thematically with what we know of the Ancients and why he was summoned.
Fandaniel:
Fandaniel is the worst antagonist of the series for me bar none, which made having to face him repeatedly all the more irritating. I like Zenos more than Fandaniel and I don't like Zenos. When the creator of the series' best antagonist, Emet-Selch, tells me he's her favorite character I'm expecting something marvelous. Instead, as someone else put it, we got "depressed Kefka" (and his tiresome attachment to Amon).
Hermes was not any more likeable either. It was obvious from the start he was an "aberration", as he put it, seemingly the only dissatisfied Ancient in their society (in large part because he was in the wrong profession). I couldn't relate or sympathize with him and, while that's not necessary for an antagonist, it is the surest way I lose interest in them. He came across as hypocritical and unhinged, which I found annoying instead of entertaining.