Recycled Script: The script is basically a recycled and compressed version of the Togepi sideplot from its hatching to Misty being forced to give it up when it's a Togetic. It's also pretty similar to the Jirachi movie.
Talking to Himself: May and Manaphy have the same English voice actress. Considering their interactions...
What Could Have Been: This movie was supposedly going to focus on Jackie Walker as the Main Character, with Manaphy being his sidekick, but this ultimately shifted to May and Manaphy's Mother/"Son" dynamic.
This was the last known major animated movie to be produced with the traditional cel animation process that had been in place within the worldwide animation industry for nearly a century. Most animation studios had already shifted to digital coloring— if not total use of digital software— long beforehand (with the sole exception of Eiken, who continued using cels for production of Sazae-san up to 2015), and cels were pretty much abandoned for all animated films not related to a preexisting media franchise after the release of Millennium Actress in 2001; indeed, the Pokémon anime itself had already shifted to digital coloring for the actual TV series in 2002. However, for reasons unknown, the films would continue to use cels for as long as possible, only abandoning them after this entry. Starting with 2007's Pokémon: The Rise of Darkrai, the Pokémon films would go all-digital, thus marking the final death knell of cel animation in the animated film industry.