I haven't played FF9 so to me the Alexandria plotline lacks worldbuilding. It comes out of nowhere and is put to rest during two zones worth of quests.

The Endless dilemma is hard to get behind, since it is not explained why exactly they need soul aether only, when there are a lot of beings that are simulated/conjured/etc. Are non-soul aether beings with memories soulless? Or Ultima Thule inhabitants which are made from 100% dynamics?

Or the regulator empowerment mode, how it related so, say something like Oversoul causing Ruby weapon to transform to Nael van Darnus?

I dislike stories where it feels like writers make up random things to advance plot but perhaps its my own fault for reading a lot of fantasy novels and being used to higher quality writing.