Until the time comes where the GUI just doesn't have the specific option for what you want to do, and then usually you can string commands together into scripts to do it. That's where its power lies. Every command/utility on a Unix/Linux system is meant to be a tiny building block to use to accomplish a more complex task.
You can't possibly program an option for every contingency into a static GUI, but you can hand the user a toolbox of command line utilities and then they can accomplish nearly anything.