So, I've been looking at Mewtwo's rpg moves and came up with some side and down B's that should be easy to make.
Please note that all these are actual moves that can be learned, none of this is created.
Swift - Side B
A multiple hit attack, Mewtwo shoots star effects out of his hand, each hit should do 1-3 damage total of 8-10 hits. I do understand this is an easily spammable move, so I would recommend adding a short recover time, so that if the player tries to spam, the foe can get away.
Psycho Cut - Side B
A single hit attack, mewtwo swings his hand and creates a blade made from psychic energy which causes 12 damage on the graphical blade, and 14 damage and higher knock back on the sweet spot, which is the hand. This attack should be quick, but again, add some recover time, but very little on this one, just enough so you can't repeatedly use to quickly rack up damage.
Recover - Down B
Restores Mewtwo's hp by 100%
Now I understand you think this is crazy, but I figured out a way to balance it. Simply give it a long start up time where you can get hit, so it can basically only be used when you kill your opponent. And if it is still over powered give a huge recovery time too, so you can use it even less.
Barrier - Down B
This should be more of a quick draw attack, like the Fire Emblem character's counter move, all it does is simply block an opponent's attack, nothing else. The move make a shield around the character, you should use the shield effect for it.
Now, those were level up moves, I'm going to start going into Tm/HM's, and because Mewtwo can learn every TM, I'm going to be rational.
Toxic - Side or Down B
Mewtwo intoxicates the opponent, or in simpler word, he give them the flower thing on their head.
Light Screen/Reflect - Down B
This is similar to barrier, except, instead of completely surrounding mewtwo, it makes a wall of light in front of him and it reflects projectiles, also, unlike the barrier, this attack can be held as long as you want, except after about 5 seconds, you begin to take damage or not either way.
Protect - Down B
Like Barrier except it gives Mewtwo super armor for a second.
Double Team - Down B
I'm serious, bring back lucario's counter, it worked, so why not.
Energy Ball - Side B
Similar to shadow ball, except it is green, can not be charged, and is small, but it deals 20-35 damage.
Flash - Side or Down B
Makes the opponent trip or turn around, or something...
Zen Headbutt - Side B
Creates a small explosion of energy around mewtwo's head, energy deals 10 damages, ears and small parts of head deal 14 damage little knock back, and forehead deals 20 damage and large amount of knock back, imagine charizard's rock smash attack.
Signal Beam - Side B
Shoots a small beam of light, similar to rob's laser.
Magic Coat - Down B
Another barrier move that eliminates knock back, but he still takes damage.
Alright, I'm done, those are my ideas and good luck!