Having you settings in a human readable format (INI, JSON, XML or whatever) has the advantage that it is easy to fix (if something went wrong), even for novice users.
(Most Windows users never ever opened the registry, or even know that it exists, als f*cking up the registry (once I accidentally removed all subkeys from Computer\HKEY_LOCAL_MACHINE\SOFTWARE ) can be unfixable.)
So, I tend not to use the Windows registry at all for my program settings.
If you don't need things like multi line values, then Ini files are perfectly OK, and easier to handle and understand than JSON or XML.
So, it all depends on your use case.
Bart