CLIs haven't been used for 15 years
Donatello, the super intelligent hacker, is saying this in the end scene when he is going to diffuse the chemical bomb.
Well, if Don was a real hacker, he'd be loving command line interfaces and would despise GUIs like every other hacker.
I know it is senseless to point out the obvious and that the reasons for this flaw are:
* Donatello was saying it to be funny or to make an excuse for himself or, which is more likely
* the movie makers are stupid