When Endwalker first came out and I played through its story, I... actually wasn't super into it, to be honest. Garlemald felt very tiny and unimportant, and Zodiark never even got to appear as a proper character.
Over time, my opinion has softened quite a bit. I've come to appreciate the stuff I think Endwalker did super well; the whole story around visiting Elpis was incredible, and I actually did wind up liking Venat's character quite a bit.
And also, I think they did a great job of exploring the themes of a truly existential crisis, through the whole story with Hermes, Meteion, and Ultima Thule.
I still maintain that the story's pacing was ultimately just too fast for its own good (it felt like two expansions' worth of ideas crammed into one), simply visiting THE FREAKING MOON would've been cool enough on its own.
But even so, and even having warmed to Endwalker's own story quite a bit more, I would still like to see two things in particular:
1. Zodiark proper
2. More internal strife of the Garlean Empire
Now in the case of Zodiark, I'm not necessarily suggested that "he needs to be the big-bad". In fact, I feel like the story kinda-sorta setup the possibility that he might've been a force intended to do good, but through a negative way. There Hydaelyn was like a loving mother, perhaps Zodiark could play more of a distant fatherly role.
Just as Light is an element representing stasis, perhaps Zodiark's influence of "darkness" is what resulted in the "Ancients" evolving into the various races we have in the present, that these forms would better suit the people of Etheirys to stand against the coming trials (essentially making the playable races a product of both Light and Darkness).
Regardless, I would just like an opportunity to "meet" Zodiark. I feel like there was SO MUCH BUILD-UP for him, it felt like a huge letdown when we only got to see him as a soulless husk inhabited by Fandaniel.
(Personal aside: I feel like "the Moon" was kind of a letdown, too, just being this massive, evil-looking crater. I'd love to be able to complete some kind of quest to give it a "makeover" of some kind, maybe growing some kind of ethereal garden in place of the giant crater?)
Also, I was disappointed to see the heart of the Garlean Empire was essentially a massive ghost-town. Again, I don't necessarily need to see them return as recurring antagonists, but maybe advancements to show Garlemald still exists in some capacity, maybe the various legions becoming mercenaries or even protectors of what little remains, maybe implying that their city is being rebuilt over time? Again, just a bummer to see what I'd assumed was going to be a massive, sprawling empire was essentially a couple of destroyed city-blocks when we arrived.
Just my two cents, obviously, but I think those are the only two lingering things that still leave kind of a bad impression for me. If the next expansion was able to pick up those threads and do something more with them, I think I'd be much more stoked.