I will grant you that. If there's one failing of P4, it's that the ending sort of comes out of nowhere. I'm fine with a late game reveal, as long as it has a murder mystery moment of "Aha! Now it all adds up!" rather than "Wait, what?"
With Nyx, however, you get a month or two to just stew and wait for her coming, and they spend that time basically driving home that Nyx is a universal constant, in a way, and is not just an entity that can be defeated. And in the end you don't defeat her, you just keep her locked away, and even that carries a pretty nasty price. Persona 3 ends better, sure, although I still prefer P4 as a whole.