Samus does poorly against MK. Aerials are hard to land on this guy. But as the others have said before, shield/dodge to jab/tilt/screw attack. Uncharged shots work well at a distance since they force MK to either shield or jump. If he jumps, you might be able to land an aerial. If he shields, you can keep applying more pressure until he dodges or somethng. After that, you might be able to find an opening. Also, platforms will help your game against MK immensely. Simply standing under one gives MK less options.