Do you have a link that would educate me about some of these problems? Package management interests me because I might find myself developing a package manager in the near future, but I don't know much about it.
Not supporting multiple versions of the same software is something that I identified as a problem though.
I don't recommend developing a package manager until you have done a lot of research. Its a field with non trivial problems and a lot of existing experience, and a lot of implementations that may well solve your issues.
Not supporting multiple versions of the same software is something that I identified as a problem though.