I wrote this on allisbrawl a little while ago so I'll just repost it. Hope it's helpful.
Here's my Snake deconstruction:
All his tilts will kill, you.
Counter: Avoid standing next to him. If you must and you manage to block him, Dair in his face. He might be slow enough that you can roll behind him and DSmash.
His nair lasts a second longer than you would intuitively think. It'll kill you. Same with his dair.
Counter: Don't run into his 4th kick -- it'll be close to the ground if it's ever going to hit you.
Also watch out for his bair. If he's in the air and his back is turned, he will either bair or air dodge if he's smart.
Counter: Come from directly beneath him when possible. Peach's Uair will outprioritize Snake's Dair and Bair. This is a good chance to score some damage or get a high % KO. Snake likes to drop remote mines and explode them as a scare tactic, but if you're approaching correctly, you shouldn't be anywhere near it. You should be able to complete a full double jump and float before he reaches the point where you can uair him. If he air dodges, you are still in control and you can chase him downward with another aerial.
Land Mine: Snake plants a land mine and runs away. You chase him, he shield grabs you and throws you in the direction of the land mine. You attack him, he doesn't grab you, you get scared and roll into the land mine because spacing is funny that way. >.>
Snake plants a land mine, you end up somewhere close to it, snake throws a grenade and explodes land mine and grenade, creating a slightly wider explosion and a pretty distraction during which he can plant a remote mine or an opportunity to dash cancel. Or he can keep tossing grenades.
Counter: Just break it with a turnip and reclaim your territory. See if you can do it while watching Snake, first. The easiest way is with a Z-drop. If you like you could also roll away a couple of paces and see what Snake does in the meantime. Then use the appropriate throw.
Remote Mine: Snake plants a remote mine rolling distance from the ledge, on the ledge, center stage, on a low platform, or on you.
Counter: Remote mines are my favorite mind game. I love to float right above the hitbox -- Snake either knows it or he doesn't. Usually, he'll just explode it. When he plants a remote mine, just bait him to detonate it if you're far enough away from him. If you know when you're going to hit the bomb running, he probably has the timing down, so expect it to go off and know what to do from there. It's a nice opening for a fair a lot of the time (NOW this). If not, Dair is still your best friend.
If he plants it on you (while you're shielding, say), just touch him one way or another and it'll get stuck on him.
Grenades: Are tricky. If Snake is backing away from you, he has a grenade and you didn't see him pull it out. Most Snakes have some visible way of cooking their grenades. My friend likes to pace back and forth, for example. There are a variety of tricks... Cook one, toss another, explode both of them. Toss one, cook one. Explode a grenade with a remote mine or land mine. Hold a grenade and let you hit him because chances are, you're the one who's going to die. Hold a grenade and roll away so that you attack the grenade instead and get exploded. Hold a grenade and air dodge into you, but that's skillz if he gets that to work.
Counter: Fear the grenade you didn't see. It's ok, but don't stop paying attention. Learn to pick up a grenade without punching it. Have the mental coolness to stop running (shield) before pressing A so that you don't dash. Know which ones to avoid and which ones you can toss back. If both of you are holding grenades, the game makes you drop yours when he throws his, so throw your grenade quickly. After you throw a grenade is a good time to approach, because he will have to defend himself.
Missiles: Missiles are a good ledge guard. They're also semi-useful for a safe landing if he pulls one out and drops it immediately. Missiles build up speed if they're going in a constant direction but slow down again if their course is altered.
Counter: Don't stall on the ledge if there's a missile out. You can easily outrun them and punish. He probably won't use them much, but hope he does.
Dash and Dash Cancel: I hate it. He has bogus range and quickness with these. If you anticipate it with your own dash, you clank. If you throw a turnip, he catches or breaks it. If you're into your run long enough that you can sidestep or powershield out of it, you can run back and catch him, unless he dash cancelled, then he's protected by a mortar(!!!). If you block it, he goes passed you, farther passed you if he dash cancels.
Counter: I usually just trot and roll in this situation and then chase him with a fair or a turnip. I think you might be able to beat it with a Dair. Two things I'm thinking might work without having tried it (it works for sonic) is to turn around when he runs toward you and shield. If he dash cancels, you might be able to grab him when he goes passed you -- if he dashes, he'll end up behind you. I think the safest and quickest way to do it would be Turn -> Shield -> Grab attempt -> C-Stick down. If you grab him, you get a free d-throw, if you miss because he dashed, you get a free DSmash. Or, you could shield it and chase his mortar with Toad.
To add some stuff... Dair combos into Dair really easy with Snake. You can do 3 and finish it off with a nair or something for some fast damage. A safe-ish approach is to start floating so that the last kick of your Dair hits him, and use that to combo into other things -- you can also be a little bit higher than usual cause the last kick has longer range. Ftilts to utilts work nice at low percentages. I tend to fight Snake aggressively, just less aggressively than with others.
Fair spammage is really effective for me in this fight since it has such good priority. My Snakes consistently live to 200% before I kill them >.> My killing moves are USmash, Uair, Fthrow, and Fairs off the edge -- fairs break through his Cypher armor.
If you're lucky, Snake will be dumb enough to use the Cypher close to the edge where you can grab him. If you grab the Cypher, you'll take some damage and Snake will fall to his death cause he can't use it again. If you grab Snake, don't attack -- just wait for him to break free as you dangle him over the edge -- he won't be able to use Cypher again. xD I've 3 stocked a few Snakes before they figured out how not to die.