First, let me introduce a new blog topic, Sysadmin where I will cover computer system administration and OS design issues, notably in Linux and related systems.
My goal is to reduce the nightmare that is system administration and upgrading.
One step that goes partway in my plan would be a special software system that would build for a user a specialized operating system "package" or set of packages. This magic package would, when applied to a virgin distribution of the operating system, convert it into the customized form that the user likes.
The program would work from a modified system, and a copy of a map (with timestamps and hashes) of the original virgin OS from which the user began. First, it would note what packages the user had installed, and declare dependencies for these packages. Thus, installing this magic package would cause the installation of all the packages the user likes, and all that they depend on.
In order to do this well, it would try to determine which packages the user actually used (with access or file change times) and perhaps consider making two different dependency setups -- one for the core packages that are frequently used, and another for packages that were probably just tried and never used. A GUI to help users sort packages into those classes would be handy. It must also determine that those packages are still available, dealing with potential conflicts and name change concerns. Right now, most package managers insist that all dependencies be available or they will abort the entire install. To get around this, many of the packages might well be listed as "recommended" rather than required, or options to allow install of the package with missing 1st level (but not 2nd level) dependencies would be used.