killing snake is not that tough. here are the most important things to remember. Trust me, these will work.
1) If you see him pulling out grenades, run up and grab him. Remember, if snake is holding a grenade, he can only do 2 things: throw the grenade, or drop it and shield. Chances are, when he sees you running at him, he will shield, hoping you will attack him and get punished by the resulting explosion. Any time you see a snake pulling out grenades (often they pull out two consecutive grenades to set up their defense), think of it as a great opportunity to hand out some good damage via a grab/pummel/throw/what ever you want to follow up with.
2) If you see snake spamming jab or tilts in an attempt to get you to run at him and get hit, use mach tornado. It will be more free damage.
3) Any time snake is running towards you, you can expect that he will either do his "snakedash" sliding upsmash, or his dash attack, followed immediately by the upsmash. Either of these can be foiled by spamming downtilt. So if hes running towards you, just use dtilt, and it should work 99% of the time.
4) When snake is off the stage, be careful when trying to gimp him. I dont recommend gimping him when he is not on his cypher. He has a really good spike, and it will beat shuttle loop if the snake player knows how to use it. Instead, wait for him to be far enough out that he has to use his cypher, then hit him with a shuttle loop. **ALWAYS SHUTTLE LOOP SNAKE WHEN HE IS ON HIS CYPHER**. He cannot defend himself while he is on it, and YOU CANNOT DIE BY SHUTTLE LOOPING TOO FAR OUT. Even if he is waaaay far out and you would normally fall to your death after using an outward shuttle loop, you can shuttle loop without fear. This is because you will hit his cypher even if he drops off of it just before you connect. Because you are virtually guaranteed to get hit by the cypher, it will prevent you from continuing your shuttle loop and allow you to use another shuttle loop in the opposite direction to get back to the stage.
In other words: BE AGRESSIVE when snake is on his cypher. Even if he is super far off the stage. Even if youre running out of jumps (dont return to the stage to refresh your jumps, just hang out and wait for him to come back, and hit him). The further out you get him, the easier it is to KO him.
5. After snake learns to fear the shuttle loop, he will often try to recover more vertically (hell start dropping in from high above the stage). This prevents you from being able to shuttle loop KO him. HOWEVER: If you are quick enough, when you see him start to ride his cypher up towards the top, start jumping up as high as you can to meet him near the top of the stage. wait for him to drop off the cypher, then catch him in your Mach Tornado on his way down. Make sure to adjust for his DI and try to keep him in the tornado for the duration of the move.... The last hit is the killer. If you can keep him in the tornado the whole time (keep pressing b), it is super easy to KO him off the top with it.
I could go on (how to deal with nikitas, how to use grabs effectively, how to deal with uptilt, etc) but those are the most important things, IMO.