* All current package managers are either language or OS specific. What if you have an application with code written in multiple languages?
* NPM didn't have any kind of integrity checks for its packages, and I assume most package managers don't either. If you download a corrupt package, for example, you won't have any idea and it will still install.
* Some package managers do better than others with regards to managing packages. I found NPM encourages dependency hell and very little management tools for dependent or installed packages.
* A lot of package managers seem to intermix packaging, distribution, and a registry. The registries tend to have limited names to pick from (like real estate) and can result in legal problems. Also if registration to the service catalog is required you cannot self-host or self-manage the distribution of your application.
I am trying to work on a solution to these problems at https://github.com/prettydiff/biddle