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.
I think the security guarantee is for the user and their credentials, not the community and trustworthiness of individuals.