The thing is, Linux distros, be it ubuntu or any other are bunch of software written all over the world, having no central design policy or architecture, put together. So making a real working and centrally controllable distro is virtually impossible or challenging. These software all have incostencies in their selves or in combinations. so solving most problems in their domains are the way to go. Because of general unix or linux philosophy of having text file based configurations, editkng these to solve most problems is unavoidable. Even gui software for configurations are generating or editing these files.

But diving and getting lost in windows registry is not elegant either..