I'd say Snake has a better Math up against MK. Maybe only just a slight amount. Like M2K said, MK only has the advatage when MK can gimp. Placing nades wisley shut's down MK's nado/pressure game quite a bit, and Snake's almight BS ftilts can outrange practically all of MK's moves. If a Snake can just maintain ground, he can win more likley. But both have one thing in each othes area. Snake has his Bair which can come out fast and unexpected, with large knockback, if he's being juggled, while MK's grab game is one of the best. If you space yourself though, your tilts can still beat out the grabs. In other words, for Snakes:
Stay on the ground all the times if can, be defensive and use nades wisley. And use your tilts like always. Oh and motars always protect you from rushing/grabs as well as gives MK's a slight harder time in the air and sometomes opens up utilts into mortar oppurtunites to rack up fast dmg.