Originally, Ash was supposed to capture Latias at the end of the film and take her with him on his journeys. It was changed so that he captured her to protect her, then release her before the film was over. A last-minute change, made less than a month before the film was released, scrapped this altogether.
For the English release of the film, the first five minutes were cut out and replaced with the same intro that had been used in Pokémon 4: The Movie (2001). The cut material showed the story from the book that Annie and Oakley were reading, entitled "Legends of the Heroes of Altomare". The story goes of how two children, who were really Latios and Latias in disguise, rescued Altomare long ago, and have been its guardians ever since.
Nintendo's largest domestic box office flop, raking in less than $750,000 in the United States. However, it should be pointed out it was only released in 200 theaters. Internationally, it earned a reasonable gross of around $20 million.