I think that the thing I miss most from a command line when I'm using a GUI is the command history.

On the command line I can use the up/down arrows to find commands that I've entered before, edit them, and run them again. I can search through the history to see what options I used last time I ran the command, and I could (if I could be bothered) run analysis to find out what commands I use most often.

In the GUI I can't do any of that. Every time I want to do somthing I need to click through a whole pile of menus and dialogs, unless the application authors have included a shortcut for the specific thing I want to do.

I probably could install a mouse/keyboard recording tool, but that still wouldn't have the naked convinience of typing up arrow enter to repeat whatever it was I just did.