In Linux you are not asked root's password to change desktop picture or installing random program and that's a major difference. Installed program has user account rights, but _that's the assumption_ and most programs respect that and, contrary to MS-systems, _can be installed and run_ just on user rights.
In MS-environment, _every_ program_ _must have_ (major) write-access to registry and system directories -> UAC every time you try to install or change anything. That's a _big_ difference. Like 1 to 100.
The idea that every program may write whatever they want in registry is outrageous. Only an idiot could design something like that.
Using Ubuntu/Fedora, you install most of the programs using aptitude/yum and that requires root password. The idea that any program can write its configuration into a centralized system (the registry) could be better than having 100's of configuration files around in different places (The fact that any program can write in any part of the registry is obviously bad).