But a few of the criticism coming from the linked blog seems of the form "the Windows Registry is only compatible with Windows".
Since the Registry is very specific to the current version of Windows the user is running I don't see why, from a technical point of view, should effort be wasted in trying to make it more compatible with other platforms or versions of Windows.
The registry is an abstraction and there's only a few supported ways to access it (regedit, .reg files and the registry API basically).