What I am speaking for here is not the CLI per se, but the fact that a CLI interface is generally a flat interface. That is: there's one place where you will be able access all of the commands, and as much the help for them.
A multi-tabbed configuration would be the worst counter-example of the former. On the other hand mentioning IDEA again - their config window (Cmd+,) directly allows one to search for the elements of the configuration in a flat manner. That's damn efficient.
Have you ever tried to scroll through a list of 100s of items? What if all of these items are in pop-over menu that closes if you accidentally click outside it? How much easier that is in a console though.
I would always vouch for software that is both easy to use right from the start, but neither does not hide it's functionality anymore: just the way we have moved from yellow pages on the internet arranged in a tree-like fashion for a purely flat Google interface, I would like to be able to use software in the same non-hierarchical way.