Mewtwo's potential custom moves were part of the pre-DLC release hype for me. So when I figured they weren't a thing for him I was freaking ****ed. Especially if it means that other DLC characters won't get any. Now I
somewhat got over it but I still refuse to believe they were judged disposable enough to just not develop in order to save time, and I'm kind of confident they'll be added in the next update. They admittedly aren't necessary to have a functional fighter, so it makes sense to put them as low priority work and release them later. It's like Squirtle/Ivysaur/Charizard's Final Smash in PM, those are irrelevant to MP's main appeal compared to Brawl (a competitive game friendly engine and balance) so they were not implemented at first but they eventually happened because they're part of each character's identity. Plus I doubt Nintendo and Sakurai will remain silent forever about this.
Anyway, while I'd be fine with generic faster/bigger/whatever variations, I'd prefer them to be mostly based on actual Pokémon moves. Mewtwo has an amazing movepool in Pokémon games, and it would be sad to waste that potentially amazing added value by giving Mewtwo's customs generic names and uninspired effect.
Neutral 2:
Shadow Aura Sphere. Yes I know this isn't an actual Pokémon move but rather a mix between Aura Sphere and Shadow Ball. I wanted to give Mewtwo Aura Sphere considering he's alongside Lucario one of the few Pokémon who can learn this move but since Smash portraits aura as Lucario's perquisite then I changed this to Aura Sphere but with darkness instead of proper aura. It works like Lucario's Aura Sphere, with the same charging speed, projectile speed and trajectory, and power, plus it inflicts damage while charging, but it has darkness effect rather than aura effect. Since Mewtwo doesn't have aura mechanic, the move's power is constant and is the same as Lucario's at 75% damage. The ball is aesthetically the same as Aura Sphere but with dark and purple instead of blue.
Neutral 3:
Electro Ball. Inspired from the move Mewtwo got exclusively through an event distribution in gen V. Compared to Shadow Ball, it charges faster (even faster than Shadow Aura Sphere), travels a farther distance, goes faster, pierces through opponents, is less powerful, and inflicts electric damage. The ball's aesthetically identical to Shadow Ball but less dark and with added electricity.
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Side 2:
Mirror Coat. Similar to Palutena's Reflect Barrier, except that the barrier has no effect on fighters themselves, the move can only reflect energy-based projectiles, and it's a more powerful reflector than Confusion with a greater damage multiplier (x1.7 instead of x1.4 and reflected projectiles go at higher speed). The move is also less laggy compared to Palutena's Reflect Barrier.
Side 3:
Trick. This move works similarly to Rosalina's Gravitational Pull, except that it only act in front of Mewtwo, and it cannot pull items in the ground. This move has more forward range than Rosalina's Gravitational Pull, by the way.
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Up 3:
Zapping Teleport. I really don't know what could be taken from Mewtwo's movepool from the actual Pokémon games that could be used as custom Teleport, so I went with that instead. Doesn't go as far as Mewtwo's regular Teleport, but once he reappears, a line of electricity brefly appears between where Mewtwo disappeared and when he reappears. The closer the enemy is hit to the location where Mewtwo disappeared, the more it takes damage.
Up 3:
Phantom Force. Yes I know Mewtwo can't learn this move in the source material, but I really can't think of a single move Mewtwo can learn that could be a variation for Teleport (which Mewtwo can't learn anymore since the gen I only TM was needed for that, but whatever). Mewtwo goes even less far than Zapping Teleport, but he inflicts a lot of damage and knockback with a darkness attack to anyone close to where he reappears. It also has more ending lag than the default Teleport.
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Down 2:
Grass Knot. Similar to Disable, but has longer forward range and can hit enemies from behind. It only makes the opponent trip instead of stunning it.
Down 3:
Future Sight. Mewtwo summons two flashes in front of him which disappear quickly, but those flashes have no offensive properties by themselves. Twelve seconds after Mewtwo has used this move, a powerful darkness explosion happens where those flashes initially disappeared. Reusing Future Sight before the explosion happens is just as useful as using Diddy Kong's down B while his banana is already on the field.
Stolen the idea of Phantom Force and Future Sight from posts above
at least on the name, I didn't read those custom movesets in detail yet to prevent myself to be biased. I'm going to read them later.