MKII Improvements:
-The rotatable hot seats have buttons of their own
-The cockpits are fully decked out with their appropriate controls
-There are a few ion thrusters hidden around so you can conserve fuel when you just need to make adjustments or precise movement in space

MKIII Improvements:
-Now able to maintain altitude and very slowly accelerate upwards in an atmosphere without hydrogen
-Now has one underside ramp that improves weight and increases durability to weapons fire
-Better handling
-More reactors so that overloading almost never happens
-Air vents so pilots can brethe in atmosphere