"Aaron 1," the song that plays during the montage of the war in the film's prologue. It has since returned for intense action sequences in the series, such as the Nando VS. Zoey battle of the Sinnoh Grand Festival.
Harsher in Hindsight: In Ash's Disney Death scene, where he hurriedly says goodbye to Pikachu and his Pokémon; this film ended up being the final entry in the Pokémon series where Veronica Taylor voiced Ash, and so the scene can be seen as the goodbye to her iteration of him as well.
Aaron's interaction with Mew in the Japanese version. Koichi Yamadera voices Aaron, but he also voiced Mew in the first movie.
May's dress for the festival, specifically her bow, certainly looks like the one her game counterpart wears in OmegaRuby and AlphaSapphire, doesn't it?
While rather dark, it's actually pretty funny that Aaron sacrifices himself to end a war without bloodshed... only for Pokémon Conquest, a game about winning them, to come out a few years later.
Ho Yay: Aaron and Lucario have astronomical amounts of this.
Just Here for Godzilla: Some people watch the movie for the titular Lucario and his storyline, leading to some disappointment after the darker, more serious opening gives way to the wacky antics of Ash, his friends, all the "cute" Pokémon, and the Rocket trio. This is interesting, as in most cases of this trope the audience ignores the story in favor of something else. Here, they're coming for Lucario's story and ignore everything else.