This particular concept is so prolific it could probably hold its own mini-Unorginality series, but I don't think it deserves that much time.
Incidentally, people really should look over Mewtwo's stat layout sometime.
Tragic Melodrama: The Chronicles of Woetwo
Mewtwo lay bleeding on the cold floor of his cell. A rocket kicked him in the side. "Pathetic pokemon," he snarled.
Such was Mewtwo's life. He'd been cloned as a replacement to the original mewtwo who had escaped. Of course, Giovanni didn't want a repeat of the last time, and so was doing this a little differently. Or entirely. Shortly after birth Mewtwo had been dumped off on a low-ranked rocket for training despite being born with enough power to level a small city. His new master was abusive and would whip him brutally for disobedience or failing to perform well enough, leaving him lying, barely able to move, in a pool of his own blood. The only upside was that he was only trained once every two or three weeks, as that was usually the amount of time it took the scientists to check him over and fix his injures. The whip tended to cause a lot of damage. In fact, Mewtwo was a bit confused as to why they whipped him rather than use the variety of restraining methods he'd seen used on other pokemon, like electric shock collars. It seemed his trainer just liked injuring him.
He couldn't fight back to protect himself from his abusive trainer thanks to the psychic-energy-suppressing device around his neck. It was apparently called a deus ex machina. With it there, he didn't have the ability to reduce the entire building to especially small pebbles at the thought. He was left only with his physical abilities, which were far weaker, being merely able to break down a few dozen reinforced walls in a few minutes.
The device was also the reason for his poor performance during training. It was hard to blast another pokemon into submission when your blasting ability is blocked to the point you can barely tip a glass over. Mewtwo wasn't too sure on what the point of the training was to start – no matter how strong he became, his displayed ability would remain the same as long as the deus ex machina was functioning, and they didn't seem to have any plans for using him with it on or ever taking it off (a wise decision given that he intended to kill them all if they did). They just kept training him and patching him up afterward.
He was in hell. Soon, he thought miserably, his trainer would go too far and kill him. Would they even care? Probably not. He was just a worthless experiment. Just another worthless, five billion dollar clone with the ability to single-handedly assure Team Rocket's victory. Why wouldn't they abuse him?
"Hey," hissed a pokemon in the cage next to him. "Mewtwo. Can you move?"
He groaned. "Yeah," he said, painfully pushing himself into a sitting position and looking toward the voice.
"Why don't you just bust out? You're more than strong enough to do it and free all of us, too."
"I-I can't. The deus ex machina..."
Out of sight, the arbok rolled her eyes. He's even stupider than his predecessor. "It's around your neck on a string," she explained patiently. "Just grab it in your hand and pull it off."