Earlier quoted context omitted.
Gnome has been replicating the worst parts of windows (the registry comes instantly to mind) since the release of Gnome 3.
I think gconf and macOS's plist have proven that Microsoft is at least somewhat right with registry, or at least the idea is. I don't know why people didn't like it and honestly I don't have a strong opinion on it, but I have a feeling in some ways Microsoft didn't have much of choice given that they need to have backwards compatibility.
personally, i think XDG_CONFIG_HOME + a robust config file framework with a standardized format (yaml/toml, whatever) would work as well. being able to specify a schema could be extremely useful, too, to prevent borked configs. as you've said, we've seen a lot of tools/OS's go this direction. and it doesn't have to be perfect, the 80% case would be a huge improvement.
i'm also sure the registry made a lot of sense at the time. it was probably way quicker than reading and parsing files. we didn't care so much about sandboxing/isolation and backing up. people probably had less application installed.