or "the registry isn't so bad", knowing full well that the registry is an abomination
How is the registry an abomination? I'm not looking for a debate; I'm just curious as to why you think it is.
A simplified abstraction of the registry is the tooltype, but rather than store named values in a shortcut (which is just an instance of the IShellLink object persisted to disk), they're stored in a centralized database.
The registry is more flexible than an initialization file, and if necessary, the two can be used hand-in-hand through mapping and redirection, assuming standard Windows APIs--GetPrivateProfileString(), SetPrivateProfileString(), et al--are used by the target application. In a multi-user system, you can work wonders with the registry at the data level that just aren't possible with initialization files. (You can get quite crafty with initialization files, but at some point, you end up with a database-like series of overlays, i.e. the registry.)
Granted, the hierarchical nature of the registry often leads to unnecessary complexity, but when used properly, the registry is a valuable tool.