The original Japanese story showed Mewtwo in a more favorable light, as feeling that it has no place in the world and so wants to "earn" its place. The English dub opted to just make Mewtwo an emotionless tyrant who wants to destroy the world, a decision that both fans and critics criticized. In hindsight, the producers felt they made the wrong decision.
When Brock states that he didn't know vikings still existed, Ash says they usually live in Minnesota. This is obviously a reference to the Minnesota Vikings football team. But in some dubs, this joke isn't used.
Producers and the director, Michael Haigney stated that there was a lot of trouble having to match the animated lip movements. The script was written twice to try and make sure that all the dialog matched up. They also said that they were very happy that Mewtwo was a psychic Pokémon, because he would converse using his ability and so there were not many times where his mouth was moving, so they did not have to work around making the dialog match his mouth movements.
The American version didn't include a section called "Origin of Mewtwo" for it's theatrical run due to its dark nature. However, it was included in the VHS & DVD releases. The VHS and DVD also had a trailer to Pokemon 2000.
When Mewtwo is shown defeating Arcanine and Nidoking, we see a shot from behind and we see the back of the trainer. In the commentary it is told that this trainer is Gary, Ash's rival from the series. They then go on to joke about his 'cameo', saying that Gary's agent wouldn't let them show his face, and that Gary is actually a stand-in in that shot.
A narrator and Mewtwo's voice were added in the American version, in the first segment of the movie, to help better explain the movie to people who may not have had such a wide knowledge of the Pokemon craze, for example parents who took their children to see the movie.
When the film was first conceived, in 1997, it was planned to be the series finale of the Pokemon TV show. However, the phenomenal reception to the show resulted in minor changes of the movie so that it would hint that the series was not yet over. In addition, it was released in theaters in-between major episodes of the show, rather than the television finale as was the original plan. (The infamous Porygon incident also contributed to this.)
The original Japanese version of the movie had a different musical soundtrack with almost no vocal songs, and many scenes that do not feature any music at all. With the English version, the music was also re-scored and was also added to the scenes that originally had silence in them.
In Japan, the main character (Ash) is known as Satoshi, while his main rival (Gary) is known as Shigeru. These Japanese names were taken from two game designers :- Satoshi Tajiri (original creator of Pokemon) and Shigeru Miyamoto (one of the head game designers at Nintendo Co. Ltd) who are in reality good friends. it was Miyamoto who pushed Tajiri's ideas to Nintendo CEOs and got the Pokemon game franchise started.
Originally slated for a November 12 release date, but the date was pushed ahead to November 10 to take advantage of the long weekend. Many posters for the movie out there still have the inaccurate Nov. 12 release date on them.
The first trailer was released in August 1999 and was shown before The Iron Giant (1999) and Mystery Men (1999). The second trailer was released in the Fall of 1999 and was shown before The Bachelor (1999).
One of the trainers who goes to MewTwo's island can be seen petting his flying Pokemon. When he talks to Ash and co. he identifies his floating Pokemon as a Pidgeotto when it is actually the evolved form, Pidgeot.
When shown theatrically and on the original DVD release, Mewtwo's voice while thinking was projected through the center dialogue channel, but when speaking to others psychically, it was projected at a larger volume through all the speakers to overwhelm the audience. The VHS, 2016 DVD rerelease and Blu-ray use a separate mix that does not have this effect on it.
The trivia items below may give away important plot points.
In the original English language version, the moral of the story is that fighting is wrong. This is one of the reasons why the film did not receive favorable reviews from critics, because many people felt this was contradictory to the series, where almost every episode has a Pokemon battle.
The "tears of life" concept comes from Norse Mythology. In Norse Mythology the god Baldr was killed by his brother Hödr. Odin sent his son Hermondr to Helheim (the world of the dead) to ask his niece Hel, the goddess of death, to let Baldr come back from the dead. Hel said that if the whole cried she would return Baldr. Unlike this movie, the legend did not end happily. This reference is possibly a reason for the use of viking-disguises for Team Rocket.
This is the first time in any Pokemon product that it involves some death in the film including Ash being turned into stone while trying to stop a battle between Mewtwo and Mew but was Resurrected by the tears of the Pokemon