Snake?
Well he only really has two projectiles that you need to worry about. His forward special and his Usmash.
His neutral special can be seen as one, but unless it explodes on you, it causes no flinch AND you can catch it and throw it back. For his grenades, you can just walk right through them(or float) and pressure the hell out of him.
For the most part, Snake's attacks are slow and powerful except his tilts and his neutral A combo, and MK is fast enough to blow through that with enough practice. Not only that, but if you use MK's air game on Snake, you can push him off the ledge pretty quickly, and from the air, Snake is pretty useless against a fast attacker like MK.
This is with enough experience and reflexes anyway. So merely a "theory" that is dependent upon the player to make it work.
MK is a man of pressure. Ignoring all else and pressuring the hell out of his opponent.