In terms of overall criticisms, I would say first of all that in a story billed as the end of the Hydaelyn and Zodiark saga, the titular primals are horribly underutilized. Zodiark is nothing but a skinsuit for Fandaniel and expresses no individual character whatsoever - It's nothing but a plot-enabler. With both him and Hydaelyn we get very long awaited (and generally excellent) boss fights, but in both cases they lack the necessary narrative payoff. Zodiark is a non-entity and Hydaelyn's fight is just a test, robbing both encounters of the weight they should have had.
Secondly, too many plot elements are introduced without sufficient buildup, specifically Dynamis and Meteion. You could say this was somewhat alluded to previously, but that's a bit of a stretch. While the Endsinger is a bit of a classic FF "final antagonist introduced in the last 10% of the story" thing, I don't think it's resolution fully justifies it's late introduction. Personally I'm not sure about the decision to make Meteion a character at all, I think people were more interested in the Sound as a force of nature or purely alien entity. FF9 didn't try to humanize Necron, and for this type of meta, existential threat that's generally a good idea I think. Though to be fair in this instance Meteion is really just an accelerating force, not exactly a root cause.
I'm sure more than a few people are irked about the almost flippant use of time travel, even if the payoff to that was pretty spectacular.
The fact that none of the main characters die, that is to say the protagonists, is an extremely questionable decision. The Scions are effectively retired anyway for a fresh start, so it's doubly confusing. But what is actually worse is the flagrant death baiting. Like, you did it multiple times in ShB already, there is clearly a limit to what can be gotten away with on this front, especially now at the end of the saga.
On the positive front, there are countless excellent moment-to-moment... Moments. Simply too many to list really, there is truly S+ execution and plotlines to be found abound. But personally I'll point out something I hardly thought possible, which is Zenos being made into a character that I really did love. Almost every scene with him was great, even if I think he kind of undermines the main themes they were going for. But at the same time I feel like this is sort of by design, and I'm a little apathetic towards the strong push for "hope good" anyway, so I guess Zenos constantly just coming in from left field to not give a shit is very satisfying.