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.
You should believe it as much as you want. I don't have any inside knowledge myself, I just remembered an HN comment that was relevant to this post and linked it.