I'm not too good with Ganondorf, mainly just play him as a fun side character, and to match up against friends who aren't too good, but I do main Snake, and although I'm not very good at alll, I'd imagine I can help a bit.
Don't bother catching his grenades. A good Snake will immediatly make you drop them right away(and put you in a painful situation if you're not careful).
If he starts planting a mine, and you're on the stage(to be honest, any not-braindead Snake player should never put himself in this situation), >B him just as he finishes planting the mine. You'll take damage, but he will too. Only do this if you have the advantage, which I doubt you will if he gets this cocky.
When he's recovering with the cypher, and you're on the ledge, just grab him. The cypher will hit you, he'll fall, and he won't be able to recover without C4ing himself(which by then, should be too late, if you're lucky). Trying to jump out and spike him won't work too well, because the cypher covers above him(it also does damage and has a fixed knockback), so you'll either have to grab him, or intercept him from below or infront. And be careful, he can get out of it at any time and still attack you.
Although Snake's got some very, very powerful aerials, he's actually not too good when he's in the air. Use this to your advantage, if you get him in the air, keep him there. Usually, he'll try to counter by dropping a C4. I also sometimes will Al-Queda with a grenade to throw my enemy off, so watch his movements constantly.
If he manages to stick you with a C4, be ready. You can do either one of three things: Touch him to stick it back to him, keep yourself in shield or invincibility frames as much as possible, or run up to him as he's about to explode it. The first option rarely actually works in your favour, since Ganondorf is alot slower then Snake, and Snake can blow it up whenever he wants. You'd have to evade him for the entire time limit of the C4(which is very long). For the second option, you pretty much have to get lucky. You do have a moment before he activates it, but he'll probably take advantage of Ganon's massive lag and activate it then. The third option is easily the most amusing, and probably the most realistic if you've got the balls to pull it off. The main idea is to keep in Snake's face as much as possible. This way, if he does blow it up, it'll hit him too. If you get stuck, you'd best spend most of your time near him. Just make sure you don't screw it up. If he hits you, and then blows the C4, it could lead to a very easy cieling KO.
Against his Nikita missile, don't try to attack it. The missile cannot be destroyed, it will only be redirected, and he can easily turn it right back at you. Your best option is just to use your shield and take it like a man. Also be careful of dropped missiles. Since he can stop the missile's motion and drop it at any time, he can use it to drop in front of someone who thinks they successfully shielded a Nikita, when all along it was dropping right in front of their faces.
Approaching will be a pain in the ***. With the capability to get 5 projectiles on screen at once, you'll have to see alot of things coming. Unfortunatly, Snake is no slouch in the close range department either. His crazy range and power will make short work of you if you're not careful. You'll have no choice but to get close as well. Your best option would be to just keep the pressure on him. Let up just a little bit, and you'll find yourself having to approach through a flurry of projectiles all over again. It may be tough, but you have no other option.
Recovering against Snake will be hard. The Nikita is an obvious edgeguard, but that doesn't make it any easier to dodge. If you actually manage to get into range of the stage, he can spam ^smash to make it a pain in the *** to sweetspot the ledge. His Bair is also one hell of an attack for almost any purpose, but it really hurts when trying to recover against it. Lastly, his Fair is slow as hell, but if you don't see it coming, it will hurt. Alot. All in all, you're going to have a very tough recovery against Snake. Especially with Ganon's poor recovery in general. You'll just have to predict what he'll use, and outsmart him. But the worst is yet to come: He'll probably have mines set up just to make sure don't get up in one piece. You'll have to memorize the location of his mines(including not only where, but what kind), and analyze the situation. It's not pretty when he has mines set up to stop you from rolling, and a Nikita coming to your face when you jump, but you've got to think of a way.
Snake's basic stratagy is essentially to get you playing by his rules. And once he has you doing that, he's pretty much won. You've got to keep the pressure on him if you want to even stand a chance.