Gnome has been replicating the worst parts of windows (the registry comes instantly to mind) since the release of Gnome 3.
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.
There's way more evil things about Windows, like click to raise and menu bars.