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 2016 Viz Media DVD and Blu-ray releases omit the Kids' WB, Nintendo, and 4Kids logos (as well as the closing Warner Bros. logo) and all of the opening credits (save for the title slide).
The VHS/DVD includes a cut scene which better explains the existance of Mewtwo, including a reference to Jurassic Park. This scene is played before the actual movie. (And makes the opening of the movie much more understandable). In the following "straight to video" DVD, "Pokemon : Mewtwo Returns" which was a direct sequel to this film, there is a longer version of this introduction introducing a young girl who appears to be the scientists daughter, who teaches Mewtwo a little bit about life. However, the little girl passes away when Mewtwo was still a little baby Pokemon, making his brainwaves violent, forcing the Scientists to rid his mind of his knowledge of the little girl, explaining his grainy memory.
In the Japanese version, there's no music heard as Ash, Misty, Brock and Nurse Joy walk upstairs to where the surviving trainers and their Pokemon are.
The American release added 'new' 3D computer animation to some sequences: opening title, the doors opening to let Ash, Misty, Brock, Pikachu, Togepi and Nurse Joy in, a CG environment camera pan when the stadium opens, Mew playing near CG clouds, and so on. The Japanese DVD and HD releases used this new animation as well: the unaltered Japanese theatrical version is only available on VHS and laserdisc.
When Mewtwo learns to control his powers by defeating other Pokemon in Giovanni's stadium in the English version, some of the Japanese animation is re-done. Also re-done is the storm sequence.
In the Japanese version, Meowth is more of a philosopher. He's poetic and he sings more than he does in the English translation. Also in this version, he's heard singing a song about the meaning of life during the credits, but the English translation just includes pop songs.