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.
While I don't want to deny the problems of not having namespaces, they will introduce a new set of problems. One issue with Github and similar platforms with namespaces is that a search for a repo turns up multiple projects with the same name under different namespaces. It's always a confusion as to which one is canonical. Another problem is that people are now going to name squat namespaces instead of project names. Imagine somebody registers the serde namespace. Their crates may be mistaken as the canonical one.