MK weaknesses: Light and easily KO'd, no projectile, killing ability is average.
Even with no projectile, he has 5 jumps, so getting around them is not hard at all. Even with so-so kill power, he has Nair, Dsmash, Shuttle Loop and Fsmash to an extent.
You talk about prevailing over the other player, you're right. But face it, there is one Snake that is on par with M2K, and that is Ally obviously. You will get the occasional stars like Lain or Dojo beating him, but think of it more broadly, not just the top 10 players of a tournament.
MK dominates everyone who isn't Snake. Even then he goes so fricking close to even with him, it doesn't matter.