This is what happens when you close Sonic Chat Room...
LOL XD
Anywho, now, I'll propose some theoretical stage counterpicks
Since one of MK's biggest assets is his insane gimping ability, picking stages that nullify/decrease gimping will be decent counterpicks. In addition, since MK is very prone to star KO's, places with low ceilings are optimal, as well.
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Yoshi's Island (Melee) is a good counterpick in this regard due to the fact that it is nigh impossible to gimp there. Also, the inclines on the sides of the stage make dsmash kills much harder to obtain for MK. The stage's low ceiling will make uair kills that much easier. The stage is just
so small, so KOing will be much easier for Sonic. It is my belief that this could, in general, be MK's worst stage due to all of these factors (and more that I am probably forgetting).
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Corneria makes a decent counterpick, as well; the place has a low ceiling, and the blast zones on the sides are fairly close to the nose of the ship and the booster rockets of the ship (aka the edges of the stage). When recovering from the left, it might be safe at times to recover onto the guns underneath the nose of the ship, as well. The proximity of the blast zones to the stage make killing much easier for Sonic, too, which is always a plus. This is also, in general, not a favorite stage of MK.
~Sonic's very own
Green Hill Zone can be another good option because of the removal of gimp kills due to walkoffs on both sides of the stage. Making good use of the checkpoints can come in handy, as well. Dsmash kills from the middle of the stage are nigh impossible for MK if you are good at teching. The high ceiling of this stage could backfire on you, but walkoffs are always an option worth considering against the king of gimp. Also, a shieldgrab near a walkoff + bthrow is always another fun way of getting quick kills; therefore, if you are good at winning those "prediction games" that occur in very close combat (for a lack of better words), then this is an option worth considering. MK can very easily turn this around on you with dsmashes and throws, too, so this is risky...
Now, before someone comes here telling me that MK has no bad stages, I'd like to concur that MK has no stages that totally wreck him; however, it is just ignorant to say that he performs on a level that is close to the best of his ability on all stages. In other words, it is still worthwhile to try to counterpick against MK.
Luigi's Mansion is a very feasible option for banning in a set against MK; he can spam tornado like no other on the bottom level, and there isn't a whole lot that you can do about it if he spams intelligently. The mansion is one of MK's best stages, too. Also, the incredibly high ceiling pretty much protects MK from easy star KO's. The blast zones are very far away from the mansion, so gimping is much easier for MK here.