I used to follow Redmond doctrines. My programs used .INI files. Then I dutifully switched to the registry - and users started complaining. So, I bucked the trend and switched back to .INI files.
Some want to edit them (good/bad?). Some want to back them up, or transfer to a new machine. Some don't want to lose them if they reinstall windows.
AS a user, I have multiple partitions. Windows/programs/data/swap (and a few others). No programs go onto c:\program files, they all go into the programs partition. No data which I can control goes into c:\user data, it all goes into the data partition (use tweakui power toy, or regedit to change the defaults (but not all programs are well behaved and read the registry for those paths - some just hard code them)).
Bottom line - when Windows gets its panties in a fankle, I do a total re-insatll (approx every three months), and I format the C: drive.
By formatting the windows partition, I get a clean install. My data and programs are safe, though I may need to reinstall a few programs, which is why I go with portable versions where at all possible.
Imo, the registry is the biggest evil ever perpetrated on Windows - a single point of failure.
My advice? Locally stored config files. INI if the user is allowed to edit, serialized or binary format if not.
Or, you could offer a choice ...