Random stuff:
Stick with the first hit of Forward Tilt. MK is often aerial, and so he'll SDI the first hit so the second would miss anyways. Rather than dealing with tons of lag, you'll shorten your lag time from 61 to 30 frames. This means you'll be able to quickly get back set up for the next attack. The routine of full F-Tilts is a poor one against MK. Furthermore, retreating Pivot Grabs are AMAZING against an aerial Mk. We're spoiled. The Marth match up is all about pivot grabbing MK, and our Pivot grab is of similar range.
Against MK don't spot dodge. Power Shield everything. If you spot dodge, you're going to get grabbed, which will turn into a down throw, which will suddenly become an edge guard. In this match up it is almost -better- to get hit than to spot dodge.
If MK is approaching, he'll most likley be doing Fair. SDI it. Force MK to only get 2 or 1% damage from you. They'll soon start to approach with Dair spacing or Nair.
If you're getting combo'ed by MK, it's because you're DI'ing wrong. Chances are you're DIing straight into MK, which is letting his relatively slow airspeed to keep you on lock down. The only moves MK is going to kill you with in the air are Shuttle Loop and fresh Nair. Most MK's of pro level use Nair to eat spot dodges and after a Uair forces an airdodge so it's rarely fresh. SDI everything. You can even SDI MK's Nair so that you're behind him. If you're hit by a Uair at low percent, SDI straight up. MK won't have the speed to chase you, and will waste a second, and maybe even third Uair in an attempt to hit you.
If you're coming back onto the stage, do not air dodge. Space MK for the U air. He shouldn't fair you, and he won't Shuttle Loop you until you take out your Cypher. SDI the Uair towards the stage, if you air dodge, you're going to eat a nair, and will probably be killed. You also don't want to get dair'ed. Recover high, save your fast fall for when MK starts to aerially approach you.
If MK is attempting to space his F-Tilt, our F-Tilt destroys it. Though their F-Tilt is a frame faster, there's something magical in the air with Snake's F-Tilt due to its massive range.
We must ask ourselves how does MK kill? At low percents with a gimp that's set up by down throws, shuttle loops that devour poor mid level recoveries, F-Smash, D-Smash, U-Air off the top, and Nair. If you are standing in the center of the stage, grounded, MK can only kill you with F-Smash and the strong side of his Down Smash. The Pro Mks kill based off of stage position. As Snake mains, we kill typically vertically and so we are not always thinking about short/long side of the stage. This needs to change. As your percentage grows, MK's throw game becomes weaker. He lacks the speed to keep up with the velocity you gain after you reach around 80%.
Walk, don't run. If you're running at MK you have ****ty options: Shield, Spot dodge, dash attack, Dacas, throw, aerials, and grenade. You have removed your best options in running which are your tilts. Everything else you can do from a run is going to be beaten by a grounded MK with Shuttle Loop or a Tornado. The only time you should run is if you're about to do a b-reversal grenade to create a wall.
If you're in the air the safest place to be is above MK. The most he can do is U-air or Tornado. If he Tornados, you should SDI and pop out, which allows you to hit the ground before MK to set up traps/punishment. If he U airs, you simply SDI as far as possible away from him. His goal in that situation is to bait the air dodge so he can Nair/Dair/fair you to the edge.
Do not get on the edge against MK. Snake's options are too limited and easy to read. MK can literally read all of the options Snake does with nothing more than a tornado. Roll? Tornado. Get up attack? Tornado. Jump? Tornado.