So I was just thinking about what his custom moves could be..
Neutral 1: Grenade- Due to limitations, he would be bumped down to a single grenade, but it would function the same as it did in Brawl, save for a slightly shorter time before exploding.
Neutral 2: Shock Grenade- Similar to Link's bombs, these grenades will explode on contact, or after a set time. Weaker than the standard grenades, but Snake can use two at a time, as in Brawl.
Neutral 3: Smoke Bomb- Less of a damaging projectile, used more for stage control/setups. If it explodes on an opponent, it will stun them momentarily, but won't send them flying.
Side 1: Nikita- The same as it was in Brawl, perhaps with some differing properties.
Side 2: Super Nikita- Faster and easier to control, but has less power. Can be guided farther.
Side 3: Set Nikita- Similar to Samus' missiles. Snake will fire out a rocket on a set trajectory that can't be controlled. Snake won't be left helpless when using this move, as he can fire and quickly run away.
Up 1: Cypher- The same reliable recovery from Brawl, Snake can still act out of it.
Up 2: Quick Cypher- Snake will fly up much faster, and cause damage on the way up. Can no longer be canceled out of, and has a shorter range but still doesn't leave Snake helpless.
Up 3: Controlled Cypher- Similar to R.O.B.'s Robo Burners and Palutena's Jump Glide. High controllability and horizontal distance, but has lower height and does no damage at all.
Down 1: C4- The same as it was in Brawl, can still stick between opponents.
Down 2: Motion Sensor- Due to limitations, it's probable that Snake would receive a new down smash, so as to not have too many bombs out at once. His old down smash would work as a custom down special, Snake plants a bomb that goes off when stepped on. Can't be placed on characters like the C4.
Down 3: Time Bomb- Rather than being a trap that Snake places on the ground, this move works more like Olimar's Pikmin. Except instead of falling off after a set time, it explodes on an enemy. It has a small forward trajectory when thrown, and will detonate automatically if hitting anything other than an opponent.