To me, the two major problems are:

1. 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.

2. 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.