A major issue with GUIs is that they are not scriptable [1], at least in the way CLIs are, like with a bash-like shell and all the stuff of the Unix philosophy [2] (I/O redirection, pipelines, wildcards, other Unix special characters that expand to, or mean, something (all of which you can use in your command pipelines).

[1] I mean, I know there are some tools to automate GUI tasks, like AutoHotkey, AutoIt, etc., but due to various window-related issues, they are fragile, I've heard.

Not saying that this makes CLIs superior for all uses, of course. Just better for some.

[2]:

http://www.catb.org/esr/writings/taoup/html/ch01s06.html

http://www.catb.org/esr/writings/taoup/html/ch01s08.html