Not gonna lie, your post made me smile in a good, wholehearted, non-sarcastic way, and you make really good points. But stealth can be negated by lighting up the room, figuratively and literally. I'll give intelligence to Snake by a long shot, but he's never dealt with something even remotely similar to Pikachu before (you could say that about all fighters on battle boards, but in Snake's case, he's fighting a speedy mouse when he's normally against...er...humans? Humans. Whatever TF Psycho Mantis is... Which his training doesn't account for). Yeah, sure he fought electric entities before, and speedy entities before, but never a small electric speedy entity that has a totally different fighting style than any human(made) thing.
Could Snake swim after being doused by a tidal wave and then subsequently shocked and rinse wash repeat?
Another thing: How do stun grenades work IRL? Are they just flashbangs? If not, Pikachu has resistance to stunning, being a master of paralysis himself. If so, Is it actual light? If so, that would work if Pikachu doesn't hear it hit the ground and has a small possibility of getting away. If it's not, Pikachu could probably outrun the blast. Heck, Pikachu can use Flash in the manga, so he might be immune to Flashbangs. And remember, if Pikachu sees Snake once, which is highly likely as only one weapon (2 if you count the different tranqs, 3 if you count stun grenades) has a chance of putting him down, and not for good, especially seeing how he has experience with knockout attacks. I'm digressing. If Pikachu sees Snake once, he's not gonna have another chance to escape. Pikachu will be on his tail and blitz after agility.
I completely forgot to bring up Double Team. I'm gonna keep it short. Use it to confuse Snake, and if Snake chooses the wrong Pikachu to target, then Pikachu knows where the attack is from and, you know the quote.