When I first moved from Windows 3.1 to Windows 95, I thought the registry was a godsend. Instead of having to hunt down hundreds of INI and PIF files to change settings, you could use regedit and configure everything from a central program manually if need be.
But the registry didn't age well and by the end of the Windows 9x era, it became a PITA to have around due to increasing complexity and the all too common possibility of massive corruption that breaks Windows.
*nix suffers from the same problem Windows 3.1 did, thousands of config files with thousands of different ways to configure them. There's no defacto standard other than the awful new Systemd that tries to stick its tendrils in everything and causes even more problems. It's getting harder and harder to find a modern SysV based Linux today that isn't overly complex to use.
I agree. Look at how it's done in AmigaOS, though. It's like a cross between the two: 'config' files are all stored in an orderly way in ENVARC: and mirrored in ENV: but they are just ordinary files that anyone can manipulate in the normal way. That kind of transparency sounds like a bad thing due to the way malware works, but really it's a good thing because the user always has very simple access to all the settings files.