This is a weird opinion, but I think that the OS package manager's complexity is largely owing to the unix directory structure which it just dumps all binaries in /bin, all configuration files in /etc, all libraries in /lib. It comes from a time where everything on the OS was developed by the same group of people.

By dumping all the same file types in massive top-level directories, you need a separate program (the package manager) to keep track of which files belong to which packages and dealing with their versions and ABI and stuff. Each package represents code developed by a specific group with a certain model of the system's interoperability.

GoboLinux has an interesting play on the problem by changing the directory structure so that the filesystem does most of the heavy lifting.