Although Mewtwo has no Custom Moves in Super Smash Bros. for Nintendo 3DS and Wii U, the game's data revealed that Mewtwo was originally planned to have them and that partial versions of his Custom Moves exist on both systems.
How to Activate
Mewtwo's Custom Moves can be unlocked in each version by importing a Mii Fighter created on a separate console or handheld. Afterwards, turn on Custom Fighters and select the imported Mii. After that, select Mewtwo, and a "Random" option will exist under Mewtwo's default fighter. The Custom Move set Mewtwo receives will be the same as the Mii's Custom Move set, meaning if the Mii Fighter uses its second set of Custom Moves, Mewtwo will access its second set of Custom Moves.
On the 3DS version, the custom Mewtwo can be kept indefinitely, but in the Wii U version the customizations will only last for one play session, meaning another Mii will have to be downloaded in order to access them again. The Custom Moves do not work online.
Neutral Special 2
In the 3DS version, this will do nothing besides make Mewtwo do the charging and throwing animations and usually crash the game.
In the Wii U version, Mewtwo will charge and throw an invisible Shadow Ball and if uncharged Mewtwo will lunge to the right, even if he is facing left, causing damage. However, if charged for too long, Mewtwo will freeze and cannot be moved. However, in certain circumstances such as being caught in a Trapping Final Smash, Mewtwo can float up into the air, though he cannot be controlled. This is referred to as the Shadow Morph. This can cause a glitch known as Stage Morphing.
Neutral Special 3
Uncharged, Mewtwo will fire a Confusion which has no effect and does no damage. If charged too long Mewtwo will again freeze. In the 3DS version, this crashes the game.
Side Special 2
This behaves the same way as a normal Confusion.
Side Special 3
This will attach the opponent to Mewtwo, meaning Mewtwo will move around with the immobilized opponent attached to his body. Mewtwo can remove them by using Psystrike, but this will render Mewtwo completely invisible.
Up Special 2
In the Wii U version, this crashes the game.
Up Special 3
On the ground, Mewtwo will fire a single Disable that will stun the opponent. In the air, Mewtwo can fire as many Disables as he wants.
Down Special 2
In the 3DS version, on the ground, Mewtwo will perform a Disable that has no effect. However, in the air, the game will briefly slow down and focus on Mewtwo as he spins around. This will allow Mewtwo to easily follow up with an attack. The animation is very similar to Mewtwo's animation when activating his Final Smash.
In the Wii U version, the same thing will happen when used in the air. However, if Mewtwo uses this on the ground, the game will crash.
Down Special 3
This is the same as the second Down Special, but this time Mewtwo is able to slow down the game on the ground as well.