Endwalker mainly confronts the ideas present in FF9, with Dawntrail doing the flipside of it, and Endwalker did it well, with you also fighting the concept of Despair, with its adhoc-Avatar being Endsinger.
EDIT*
Also I have to add, almost every single Final Fantasy is a clash if ideals and concepts, none of them are face value, at least not past 4, 12 is not just a band of people fighting an Empire Usurper, 7 is not just the group fighting a science experiment...
I can’t comment on 14 but the best villains in the franchise are symbolic without being symbols themselves. I think that’s why Necron felt like he was out of step.
Sephirotj and Kefka represent things while being characters for ex.
I think the disconnect here is that I don't think Zemus started a cliche or pattern.
Your mileage may vary and that’s fine.
As a storytelling device, where the climax goes to a bad guy who feels distant and unearned, I would say IV does. For the reasons we agree. We get a new villain controlling the old one and even he changes forms and considers himself a new entity. That’s like the standard. Presumably the difference is that Zeromus would kill the Moon People too. Not just Earthlings.
I would count V because the dialogue does imply that Neo-Exdeath has a different motivation (to destroy all) and the old Exdeath was absorbed. You can disagree here but it doesn’t come across like Exdeath just assuming his final form by being usurper/skinsuited. Exdeath wanted to rule by becoming a living WMD, but not actually destroy everything.
6 and 7 have the most iconic villains, who buck this trend. With Sephiroth even assuming control of Jenova through his Will.
Ultimecia does feel tacked on to me but it’s hardly why that game doesn’t click. She does follow the pattern of a secret villain who is either released or was behind everything but also doesn’t feel that different from the big sub-villains. However it is at least spaced out so you can warm up to it.
9 has Necron. He isn’t similar to Kuja so you can at least argue we get something in the trade.
Yu Yevon. He is tied into the Lore in a way that feels essential. However his boss fight is bad enough that Braska’s Final Aeon feels more fitting thematically just by dint of that.
Vayne transforms into the Undying but as far as I know any significance to that begins and ends with the name.
13 has Barthandalus doing bad but Orphan being the real power. I don’t know if this really counts or just superficially fits the pattern. And idc about the sequels to know.
And 16 pulls Ultima when the Dominant of Odin fit the attempt at being down-to-earth.
It’s like the magical heroines. Not always the case but it’s wild how often they do it even when it doesn’t seem like they want to.
I think you are saying something incorrect and either intentionally misreading us or not making a clear argument.
Either your problem is that Final Fantasy games have a tendency to have twist villains whose presence is fully felt only at the finale, in which case you are right to say Zemus's appearance at the end of FF4 is not the best way to make him be a mastermind, or you are arguing that Final Fantasy relies too much on having the final boss be a completely different new guy, which does not apply to Zeromus because it's literally Zemus pulling an Obi-Wan and letting Golbez and FuSoYa kill him so he can go full spirit. His soul is so full of evil and hatred that he becomes an embodiment of it, but this is the exaxt same as the Emperor of Hell from FF2 being an evil ghost thing. By comparison, Xande and Cloud of Darkness are NOT the same being, neither are Jenova and Sephiroth or Kuja and Necron [for the examples I care to mention].
The thing that makes me “wrong” Is not Taste and Role in the Narrative but the Lore being slightly different even as the story fits a common structure at these points. Figures.
I also don’t really consider it a problem. It’s just why I would consider IV part of FF’s Origins instead of when the series really ran with its identity.