The Cmdr sitting in his cockpit has in front of him a hotas NOT A DAMN MOUSE AND KEYBORD.
"These are the adventures of the new spaceship Enterprise, where Ensign Max is using Mouse and Keyboard to travel far worlds, fight evil forces and chat the Enterprise forums, like no one has ever done before"
I have seldomly seen a Joystick at Startrek actually. I remember one time, when the first Commander uses a single Joystick to manually fly. When the Enterprise ganked, they did it by Keyboard ;-)