I agree with you (well except for the Primal Spirits that I removed from my 4e games as well). However, when you said, "But it’s very, very different than how I would run Nentir Vale." It implied to me that there were some changes you might make.
I don't see the need to change it because a change of editions either, so let me re-phrase the question:
How would you change the Nentir Vale cosmology?
Ahh, I see. In that case, what I would change would be similar to what you say you would, particularly the part about not trying to include every story that eventually got referenced throughout 4e’s run. I’d pair it back to the core ideas of the setting and restore some of the mystery. My guiding philosophy, if I were to redux Nentir Vale would be “folklore, not history.” The Dawn War, for example, defines a great deal about the setting, but as 4e went on, the events of the Dawn War became more and more clearly defined. I would make it, rather than a historical event that objectively happened, a common element that occurs in myths throughout the world. Much like how in real life, almost every culture has a Great Flood myth, I would have every culture on Nerath have a First War myth. And many of those stories might have common elements, while many others would contradict each other.
One of the biggest changes I would make would be to break up the pantheon. In keeping with the “folklore, not history” design directive, I’d have different cultures revere different entities, some of which might share common elements that might hint at some deeper truth, but I wouldn’t have any objective facts about what that truth is, if it exists at all.
So, take for example the story of Asmodeus’ betrayal of He Who Was. Maybe the dominant religion in Bael Turath was originally monotheistic, and dedicated to this forgotten god, now remembered only as He Who Was. Maybe this religion was eventually displaced by the worship of nine divine Princes. And so, they might tell stories of an overbearing god who demanded his followers reject all other deities, but was justly overthrown by his angels, who brought order and prosperity to the Turathi empire. Meanwhile, the Dragonborn might say that these Turathi gods are devils, to whom the Turathi nobles sold their souls to secure their rule, turning their backs on the one true god, IO, in the process. Meanwhile, the polytheistic Nerathi might say that He Who Was was originally part of their pantheon, before being killed by Asmodeus. These conflicting tales, when taken together, paint a picture of what may have been, without giving any hard answers, and makes the Nentir Vale a bit less of a monoculture.
Actually, this idea of how I would modify Nentir Vale cosmology was the initial inspiration for my homebrew setting. I’ve changed all of the names, and a lot of the details to make it my own, but many of the core ideas can be traced back to Nentir Vale.
