I think you're doing good work here, and I agree that PyPI is quite a bit of a mess. One little suggestion/question, though.

CPAN: Comprehensive Perl Archive Network

Rubygems: (self-explanatory)

PyPI: Python Package Index

Crate.io: Crate? Crate.io?

Nothing about the name or any part of the domain really mentions Python, or Python packages or libraries. It's not a bad name, but it doesn't really seem like a name for a large Python package index. What's the exact rationale behind the naming?