The non-hierarchical, not-reused, reinvented package convention. The most popular package repository being incredibly hard to find one package you want among a sea of crap. The lack of a single standard solution to the most common problems. Frequent backwards compatibility issues.

It's definitely not the worst. But it's hilarious how bad it is considering how popular it is and how long it's been around

Is the fact that there are multiple package managers for the same package fornat/spec the reason why people say it's a mess?

Genuine question: How is PyPI different from NPM, Maven, crates.io, etc..?

Why "Python packaging is a mess" and not the others?

That so many things doesn't run on the latest stable version is one of them. Python 3.11 was published in all the way back in October, and it's still not stable and well supported.