Oh gawd, you really can't help yourself can you Mixture?
What's that, don't like the sound of truth ?
What difference does it make that the whether the GUI sits atop a command line or not?
I think you know exactly what difference it makes in the world of software development.
Heavily compartmentalised software development with different teams of developers developing different packaged products and all operating independently (since the various Linux packages are all independent projects) with no central management or project management structure is not exactly the recipe for building a coherent desktop operating system that the average non-technical user will find usable.
As they say .... you can't polish a turd, but you can roll it in glitter.
That's exactly the case with Linux desktops. Sure you can make the GUI all fancy pretty.... but if your development style is to wash your hands of what's going on in the backend then you're never going to be able to deliver a final product that's anywhere near as integrated as Windows or OS X.