I think my biggest disappointment with the middle part of the MSQ in Garlemald was the lack of any mention of what happened in the 6.0 combined role quests.
It's even relevant, because the same lessons are taught there as with what happened in the 6.4 MSQ. Garlemald needs to figure out what they want to do from now on, as a sovereign nation, whatever it may be. Nero even gave a whole speech about how "Garlemald did not rise to grandeur from complacency in the present or rumination in the past. We live for the future. It is in our blood." Whether or not this is actually true or part of Nero's personal delusions, it's still a view expressed in the game dialogue in the usual philosophizing cutscene tone, so it's something that we're supposed to at least consider. And seeing the same sentiments repeated here means either players will feel that this is a retreading of old ground in 6.4, or the combined role quests are retreading old ground after 6.4.
There's also no dialogue that I can find regarding the "former senators" of Garlemald who went to the Moon. They're even still there (in the Carrotorium, going through Loporrit shock), but their existence has been forgotten by the senators still in Garlemald?
Unrelated to everything else, but for the 6.x MSQ in general, I've been replaying the FFVI Pixel Remaster, and I'm finding it amusing how the description "half-human woman tries to understand emotions and social interaction, by asking everyone she meets what is love, regardless of appropriate context" matches both stories.
EDIT: (forgot to mention, but just reminded of it)
Pandemonium:
When we learned that Athena allegedly used a part of Azys Lla to rebuild Pandemonium in the present day, did anyone else port into Azys Lla to check which portion it was?
I did look around, especially in the Flagship area around the Aetherochemical Research Facility dungeon entrance, but I admit I'd never really looked at the place before, so I honestly have no idea if anything was missing. Or if anything was put back when we finish the raid series.