Just finished the game. I'm not a huge fan of the ending forcing you to either way allow the wheel to be broken, given that that was the impetus for the whole campaign.
What I do like, however, is the clearly cyclical state of the world the plot implies.
Back in Pillars 1, we learn that the Engwithans, at the height of their power, were master animancers, among other things. They got so powerful in just about every imaginable walk of life that one day, when they said "Hey, lets look for god!", it was a perfectly viable thing to do.
Only, they didn't find god. We're told that they found either god(s) was dead, or left a long while ago, which drew their attention to the need to "fix" the cycle of life.
Interestingly, fast forward several millennium later, we are in a world where animancy is on the rise. Perhaps not super advanced, but definitely catching up. The gods notice this. Somme are afraid of where it might go, some shrug indifferently, and some want to encourage it. Eothas in particularly wants to see it thrive and see Kith arise to the responsability of running their own world without the current cast of gods, up to and including destroying the current machines of soul control. Which is going to lead to a dark age in which the gods weaken, possibly die or simply go away, not being needed any longer. Which might lead to a time when Animancy is at its zenith, but so far removed from these events that the mere memory of the gods or what transpired in Deadfire is long forgotten. In turn, Kith ask the same question the Engwithins did, and learn that the gods are gone. And so the cycle repeats itself.