This is just my opinion, and I'm not saying the ending is flawless, but I guess said flaws bother me very little. And the more I think about it, the more I like it, and I'm thinking its actually one of the best endings to any RPG I've ever played in a long time (for me personally). Keep in mind that I'm looking at the ending in broad strokes, and I can't help but love it.
I love the feelings of powerlessness and inevitability that I felt when finally confronting Eothas (both the first time in the Ashen Maw and again at the end). I love that you can't stop him. You can't dissuade him. He is set in motion and all you can do is adjust to his ending and build around it (ie, the rest of the ending slides).
I've played so many RPGs where I'm this entitled, all-powerful, world-determining, Special One that I've frankly gotten sick of it. Deadfire was refreshing to make me feel inconsequential in regards to this massive cosmic force. Like I was just along for the ride. This was more immersive for me than any other RPG I've played in a long time, as for once I wasn't literally the strongest being in the world. This made Eora feel bigger, not smaller.
I also love not having every single minute question answered. Why should I know the answers to every mystery and physical/metaphysical law of Eora, souls, etc? After all, I'm just a mortal, and not even the Gods know all the answers. I knew more at the end of Deadfire (significantly more) than I did when I started, and this was enough. Not having all the answers allows me to speculate, as I did in PoE 1. Again, this makes Eora feel bigger, not smaller. I know at least Wael would agree with me.
And finally, I love that I could not foresee the consequences of my in-game decisions at the end-of-game slides. I love some of the things I did actually had unintended negative consequences... like I'm not this all-powerful seer who can literally shape the future with my mind.
This altogether makes Deadfire feel like a real world, and I'm just someone one in it. I love it.
Besides... I still ended up having enough influence to literally determine the political landscape of the Deadfire Archipalego in deciding which faction runs the show (and in my case, even the leadership of said faction). This is kind of power is plenty (maybe even too much).
This is just my opinion. Different strokes for different folks and all that.