I suspect if the concept of the registry was created today it would look more like a database (e.g. Sqlite), although organizing it like a virtual FileSystem does have a certain appeal, and unfortunately I don't know of a database engine that supports such a layout. The Registry's Key-Value pairs are 1:1 with a database table's column-values pairs, it is just the multiple tiers of organizing "folders" above that that are a difficult implementation detail.
The UNIX way is undeniably more flexible since it isn't a virtual filesystem, it is just a filesystem. The problem is that everyone invented their own configuration format to store configuration data in /etc and there's no format agnostic API to access that information (you can open it, but can you understand it?).
Both UNIX and Windows suffer from the same orphan issue wherein information can be written, the application removed, and it is unsafe to ever remove it since you may not know the author and or all consumers.