To me, the two major problems are:
- no namespaces
Someone uploads "serde2"? that's blocked forever. Someone uploads a typo version of a popular package? Too bad for you, learn how to type.
- the github connection
If you want to contribute to crates.io you're bound to github. No gitlab, codeberg, gitee, sourcehut, etc.
Not sure if there are any other problems, but those two seem like the biggest things and #1 is AFAIK not something they ever want to change + it would be difficult to as one would need a migration strategy.
For #2, there isn't anything stopping a separate auth system not through GitHub. Really just needs someone to own the implementation. See https://github.com/rust-lang/crates.io/issues/326#issuecomment-216662599 for past discussion surrounding this.