The Japanese version's Mewtwo is shown in a more favorable light, feeling that it has no place in the world and so wants to "earn" its place. The English dub opts to make Mewtwo an emotionless tyrant who wants to destroy the world, a decision that both fans and critics criticize. In hindsight, the producers felt they made the wrong decision.
The Japanese version has an entirely different story.
Producers and director Michael Haigney had trouble matching animated lip movements. The script was written twice to ensure all dialog matched up. They said they were very happy Mewtwo was a psychic Pokémon because his mouth rarely moved, which saved them work for making dialog match his mouth movements.
When Brock states that he does not know vikings still exist, Ash says they usually live in Minnesota. This is a reference to the Minnesota Vikings football team. This joke is not used in all dubs.
A narrator and Mewtwo's voice were added in the American version's first segment to help better explain the movie to people who may not have had much knowledge of Pokémon (for example parents who took their children to see the movie).