"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.
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?
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.