It does seem the prevailing writing style of academia is a big part of the problem. Papers a lot of time leave the reader feeling stupid. “Surely there’s wisdom here!?” the reader hopes. Maybe if papers taught the underlying concepts in a clearer, more transparent way we’d get better, more reproducible science

This is also a recent phenomenon. If you go back and read papers from 50 to 80 years back, they are shorter, more concisely written, mostly devoid of confusing language, and they are a pleasure to read, rather than a chore. It also comes from the practice of writing solely in the third person; it wasn't previously common, and authors could freely express their own opinions and thoughts directly without hiding them behind flowery language. With the extreme formalism of today's papers, it's made them sterile and devoid of any human connection.

Today, it seems that using unnecessarily complex language is required to make work seem more impressive than it really is. Perhaps because much of today's published work is not that significant. I've been asked to rephrase perfectly clear and simple sentences solely to use fancier language and currently in vogue vernacular. None of that aids clarity or understanding.

That's really up to the reviewers. I've definitely been told that I need to clarify different parts of my paper in my reviews.

Ultimately, peer review is only as good as your peers. If they won't call out bullshit, then bullshit gets published.

I wonder if the code was not working, how you plot the results?