Samus <.< If your not using mines if hes spamming tornado your not doing it right. Spacing is key as well as mine placement and missiles. Full charged shots stop his spin and tornado. ZSS isn't bad either, you can time her >B Just right to hit him or grab him because of the range, only problem is he can fly over your Recover, so if your coming in low you bet yourself a stock is gone.
Quick simple facts about MK
Most MK's will approch you with a quick running A or Grab. Most rush in blindly unless spamming tornado and blah blah. A dtilt with Samus or even a quick run with ZSS to meet them normally catches them off guard. They do not expect Dtilts range with Samus to reach that far, typically I follow up with Fair combo missile to keep pressure, typically thats when the tornado comes in, ill drop a mine, retreat, rush, Zair, follow and repeat. I really do not have problems with MKs.
ZSS - I will always keep pressure. Using UpB to yank them down when they do shuttle loop is LOL city. If they rush don't be afraid to use Dsmash to stun them and land a nice Forward smash on them for a punish. If your space and play your cards right, youll be fine.
Samus VS MK -
http://youtube.com/watch?v=yFLIX9vigp8