I keep a Gnome Shell instance always running with a Screen session. However, what I actually use to run CLI commands is Emacs Shell, built-in to Emacs.

Emacs Shell has most of the bells and whistles you get from things like Fish shell. So I like to use Dash, a minimal POSIX shell that is much lighter weight than Bash, Zsh, or Fish. Dash provides no features -- no tab completion, no history, no line editing -- and I have Emacs add all of those features on top of Dash for me. It is amazing what a good, scriptable terminal emulator can accomplish.

Emacs Shell can be scripted using the same scripting language it uses to script the editor, file browser, window manager, and everything else. So you can script the shell to search for regular expressions and make things clickable with the mouse, or only display portions of output, creating simple interactive views around shell commands. You can bind certain click buttons or keystrokes in the editor or file manager to run shell commands in new windows. You can script the shell with "expect"-like behavior (automatically input responses to certain prompts). You can capture and collate the output of multiple commands running in parallel.