My understanding of Johnny Five is that it's a way to drive an external board from a "normal" computer. So you aren't putting any execution (or JavaScript) onto the Arduino (or other embedded) controller. Instead you load their premade firmware onto the controller, hook that controller up to your computer via some serial connection, and then the Johnny Five library lets you control everything from the main computer.
It seemed kind of trivial when I first heard about it, but now that I've experimented some with these things it's not that trivial, and it's a reasonable approach. Especially for robotics – an Arduino board isn't a good way to drive a robot (too limited), but it's a good way to drive many (but not all) of the specific components you might want to control. Then the real brain can be a Raspberry Pi or some other proper computer.
It seemed kind of trivial when I first heard about it, but now that I've experimented some with these things it's not that trivial, and it's a reasonable approach. Especially for robotics – an Arduino board isn't a good way to drive a robot (too limited), but it's a good way to drive many (but not all) of the specific components you might want to control. Then the real brain can be a Raspberry Pi or some other proper computer.