If I remember correctly there was an internal effort at Microsoft to scrap the registry (Longhorn?) but they decided not to, and probably because a registry is actually a good idea and necessary to get something performant (compared to ini files).

The critique against the Windows registry stems from the Windows 95 days when the registry could become corrupt and repair or reinstall was necessary. However since then the registry works like a database, it has transaction logs and simultaneous writes are atomic. Registry is also strongly typed, not a bunch of strings. Registry can easily be backed up and restored.