Honestly, the registry is no worse from an end-user POV than the /etc filesystem under Linux. In point of fact, given the diversity of file formats and sources in /etc, it's probably fair to say that the registry is equally navigable and understandable to the average Windows power user as the config tree is to a Linux fan. Because keys are typed and support ACLs, it's also arguably better-protected against accidental or intentional breakage.
If you want to attack an ad-hoc config system, then perhaps talk about the mess that is OS X 'defaults', or GConf's half-assed reimplementation of the Windows registry for GNOME.
That being said, I am most certainly not a Windows partisan. The last time I worked primarily on a Windows system was when I worked for a large hardware manufacturer, and the entire company ran on Exchange + Office. That was over five years ago, and I have been almost 100% on Mac OS X + Linux in the meantime, with only occasional use of Windows in a VM to verify IE compatibility.
The reason is this: for the tools I need to be productive (Vim, Ruby, Java, Firefox, MySQL, IM client, email client) Windows is at best equally capable, and at worst a second-class host, to Linux. OS X is about as suitable a platform for those tools, but has a much smoother media (esp. online video) and mobile story. Hence, the advantages of Windows (huge application library, obscure HW compat) are largely moot, while its disadvantages (poor POSIX/UNIX compat., weird dev tools, cost) are more apparent.