Math Combat Challenge will be H.O.T.A.S. compatible. HOTAS is an acronym for “Hands On Throttle And Stick”, and you can find them in modern fighters.
With a HOTAS, you can control your airplane, or here the starship, directly from the HOTAS controls. You can concentrate in the enemy, not in the cockpit instruments.
In fact, almost all the betatesters are fighter pilots, and they don´t use gamepads, but HOTAS. And yes, gamepads will also be compatible of course.