Have you watched Ponyo or Princess Mononoke? Those are pretty coherent throughout, the pacing is way better in those, and the writing is almost flawless.
I have watched them both, and I can’t remember Ponyo very well, Mononoke was awesome with some slight weird pacing from my memory of it.
They were both pleasurable to watch!
The ones I can think of where I questioned the pacing is Earwig, Pocco Rocco, the other airplane one, the small people one, and there are a few others I may be forgetting.
Call me Original™️, but the pacing of Spirited Away was fantastic!
As for stories, the only story I have actively disliked is the earwig one. To me, that movie made absolutely no sense.
Granted, I know these movies must be going over my head, as I don’t have a firm understanding of the Japanese people and their culture. I just really love their art style!
I think you need to be aware of some background about Miyazaki to appreciate some of the details in the movie. For example he was in a firebombing during world war 2 as a child. Additionally at the end of his career he was looking for a successor to take over his fantastical kingdom and there is a metanarrative about the creator having to let go of the world he created.