Hi,
This is a long old debate where industry take swings every few years. The OS guys can't live without registry while application developers want everything to be in configuration file. What really required is a coordinated effort to define a framework in which we can utilize best of both worlds. I've written an article on the subject & I hope that It can help create a system in which every stake holder OS, Developer and User can exercise their expertise easily. My complete article can be found at
Registry or Configuration files | G3itcon - Open Source and Linux solution provider