I find the griping a bit over the top. The point of the OP is that new exciting improvements have arrived in the Python packaging infrastructure. Yes, there were many ugly overwrought things in setuptools' past. Yes, npm has several great ideas. npm is also much younger than setuptools/PyPI, and I can cite lots of horror stories from its pre-io.js days too. But the volunteers who got us this far deserve to be recognized for the progress they've made.
I think the biggest legitimate concern right now is how unintuitive it is to use pip in the presence of several Python runtimes/versions.