There no real control of what and how you installed stuff. This create long term issues. This is why you perform registry clean up. But it is not enough, because of orphaned and conflicting dlls, inconsistent installation paths, conflicting versions. You probably don't see just because you are used to the issues and you think that's how things work.
If you install a better os, everything is accurately and centrally managed, making maintenance much more easy. Problem is with closed sourced software and drivers, because they break the normal processes of installation and maintenance, creating similar issues as in windows (not as bad because the os is better engineered)...