Mewtwo was a new form of treatment, done with electric impulses and a machine to knock Ash out of it, taking down every last one of his mental guards (the original pokemon in the movie).
In Ash's mind, Mewtwo and his clones were the treatment for the mental safe guards that were protecting Ash and keeping him comatose; the pokemon of his world. The clones were counters to Ash's mental safeties, and so each appeared to Ash as the exact copy of his defense, intended to take it down by Force. The clones didn't play by the rules of Ash's world, they didn't use any special pokemon attacks or moves -they just beat down their counterpart by brute strength.
The treatment was working, but there were side effects. The electric jolts were beginning to effect Ash's nervous system, and if the treatment continued, he would be paralyzed. His mind realized this and manifested it to Ash by petrifying him in his dream. Were it not for the end of the treatment by Ash's mother (knowing her son would never want to live in a world he couldnt explore) Ash would have remained as stone in his dream.
After this, Ash needed to recover from the damage of the electric therapy. Obviously it was greatly dangerous to him, and in order to reduce the danger Ash's conciousness felt from it, Ash's subconcious began downplaying the effects of electricity in Ash's world, which is why Pikachus electric attacks -once noted for their strength by team rocket- no longer have any effect on Ash, other than comic relief.