While I doubt MK is god tier material in P:M. Here is an obscure idea to make him a riskier character.
How about MK can only do one aerial attack per double jump? Now I know that most MK players do a dair, uair, in conjunction with all of MK's jumps, but think about what kind of changes this makes in MK's game.
1. As soon as MK aerials, he has one of these choices: Get to the ground, Jump again, glide, or special fall in one of 5 different ways.
2. In conjunction with 2, if opponents play the bait game against MK and get him to whiff, then prediction becomes quite simple and only gets simplier the higher MK goes. This also means that evasive action will not reward MK players who are putting themsevles at risk with each jump.
3. MK will be incredibly vulnerable to juggling if he has used all of his jumps and his last aerial. This will be his true weakness and the key to fighting MK: force him to use all of his jumps.
4. MK players will have to be more precise with their attacks since they will always be forced to jump if they want to try again.
5. Hitting the ground or ledge is even more rewarding.
Of course, I am not even sure if all of these factors will go into play and make a difference... (or be possible to code for that matter) what I am certain of is that (if this gets impletmented) that MK players will be urged to develop an onstage game more and make evading an exploitable weakness.