The controller is because they aren't integrated into radar, or the target doesn't have enough of a signature, or it's not in an area the radar can see, and AI

The controller is because they aren't integrated into radar, or the target doesn't have enough of a signature, or it's not in an area the radar can see, and AI vision isn't good enough to pick them out of the image yet. Also, you want to be able to tell the system to hit target X, not target Y, because X is a bogey, while Y is a friendly. A Phalanx CIWS can do fully automatic against a missile, but there's other targets you might want it to take out, like small boats. So they have an electro optical sensor to see, and a controller to let them aim it manually. As to why a video game controller? Because they're cheap and people already mostly know how to use them. Mice might be more precise, until you're bouncing along a dirt road, or in sea state 5.