Brandon makes some good points. I'll add a couple points of my own that some may take for granted:
o For a user interface to be friendly, it has to in fact be runnable. Window system interfaces tend not to work well on text consoles or in environments where the user is running on a different machine which for various reason't can't display a remote X session from the server. Some sites have draconian policies against X libraries even being installed on servers o An increasing number of graphical interfaces these days are being done with gtk/GNOME, which effectively limits them to running on Linuxes. Of course, the existence of a graphical interface doesn't really preclude the continued existence of the CLI, but one might worry about the latter being deprecated.
