The Gods and this Metaphysics too often began appear in the plot in order to inflate the importance of everything and everyone. Most of these stories are actually empty and do not carry any meaning = real influence on the game world.
Pillars of Eternity is good without it. And all this pouting importance about the gods only harms the universe.
On some basic level I somewhat agree with you - I don’t think Deadfire handled grand universe changing story well. More time is given to a conflict in the Deadfire - it’s more fleshed out, characters in game care more about it. The destruction of the wheel is somewhat damaging as it makes the central conflict of the game somewhat irrelevant. Now, what I just say is not quite true - conflict in the Deadfire ties to ways you can influence Eothas. But I don’t think it works as well as it could/should have.
I disagree strongly that PoE should drop the grand ideas and be just a fantasy adventure. PoE1 showed what great universe it can be. Even though it’s heavily flawed I find Deadfire far more interesting than most IE of old (except Planescape) or something fun but incoherent like Divinities. It might be a matter of taste, but if anything I wish for any future PoEs (if they happen) to explore its ideas further. I think that not being able to stop Eothas is not an issue - not being given enough space to process, understand and react to it (and have the world react to it) is. PoE companions and world well resonated with the reveal. Deadfire god content feels a bit too much like lore, and not enough like a story.