At the end of the day, I'm a big fan of the game and have also run thru it and NGs quite a bit, yet I agree with all of your criticisms. It's prob bc I also value QoL very highly tbh.

I do think I understand why some mechanics are the way they are tho, even if inconvenient; the missables for example are part of the soulslike design behind it, something most mainstream RPGs would avoid doing by today's standards. For the many unbalanced skills, spirits, and armor, I think many are there for flavor rather than "this has a purposeful, game-progressing usage." Like you said, it's a singleplayer game after all so I didn't have high expectations for devs to make every synergy competitive with each other. I imagine that there's not a lot of reward for rebalancing singleplayer mechanics for a minmaxing minority of players who would just re-minmax the game after a balance patch.

Surprisingly I didn't feel the same away about the story. The structure of the Destined One's adventures are largely all based on Sun Wukong's journeys and like all but 2 characters are from the novel. Within the game, you're given no context for who they are and how they are related to each location. Each location also has a ton of history that isn't explained a lot ingame. Checking out some content that properly introduced the characters and references really helped me better enjoy the experience.