I think one of the major things that the CLI has in its favor is the ease with which an experienced user can guide a new user. The experienced user only needs to the tell the new user what to type, and when to hit enter, which can easily be accoplished via phone, email, IM, etc.
Navigating a GUI over the phone is a skill that few possess.
Recently I had to perform a very simple image manipulation: given two images, I wanted to use the second one (which was all grayscale) as the alpha channel for the first one. I spent quite some time googling for things like [gimp alpha channel] and reading various tutorials, which were very nice with screenshots etc. and still I couldn't really replicate the process. Then in a flash of genius I replaced "gimp" with "imagemagick" in my query. The first page Google took me to contained a command line which I copy-pasted and it did exactly what I needed.
Navigating a GUI over the phone is a skill that few possess.