I've used a Joystick, Xbox controller, Pedals, and throttle. Along with various combinations of those.
Overall I thought the Xbox controller was comfortable and fun. Yaw into roll isn't ideal, but with practice it's not hard to control if you yaw or roll. Controller flying turned my space trucking days into a breeze and was sufficient for combat. I felt the xbox controller was lacking a couple axis of control so I tried adding pedals to control yaw and vertical thrust. That made for great flying! It really had potential for aiming and flying, but adjusting ship speed wasn't the quickest. This was made up for slightly by the fact the right thumbstick was able to control forward/reverse thrust so I could throw that backwards or forwards to temporarily and quickly adjust speed.
Nothing beats a throttle for speed control, if your able to swing a hotas I recommend it.