- Artist Disillusionment: Reportedly, the movie's scriptwriter is not taking kindly to questions about Newtwo.
- Colbert Bump: Indie actress Miriam Pultro voices Mewtwo in the English dub. Ironically, this movie and the whole controversy surrounding it helped raise awareness of Pultro and her other work, and consequently gained her a small following for being One of Us and for taking the whole Mewtwo controversy with grace.
- Cowboy BeBop at His Computer: It's not difficult to find online reviews that are under the assumption that this movie's Mewtwo is the same one as the original with an unexplained sex change and case of amnesia (though it's not like the movie itself tries to differentiate the two beyond their voices).
- Dueling Movies: With Monsters University in Japan. Despite the creators' confidence in the movie's success, Monsters won out.
- Fan Nickname: The Mewtwo in this movie is referred to by fans as "Femtwo", "Newtwo" or "Mewtwotwo" to distinguish her from the original.
- I Knew It!: Sort of - due to the similarities between Genesect and Mewtwo (especially its animé counterpart), many fans believed that if Genesect got a movie or otherwise significant representation in the animé, Mewtwo would return to fight it. In the end, they were half-right - they got a Mewtwo, but not the one they wanted.
- Jossed: Even after the movie was released and all was said and done, a few fans thought that Mewtwo's new form must be Psychic/Fairy-type, explaining its feminine voice and personality to a minimal extent. Turns out, Mega Mewtwo Y is pure Psychic.
- Missing Trailer Scene: By now it seems to be mandated by Japanese law that Pokémon movie trailers have at least one. Each of the Japanese trailers had some, and the English trailer is made up entirely of these:
- The Genesect Army being created in tubes similar to Mewtwo (as opposed to a more elaborate machine with coffin-like pods) and fleeing immediately upon activation.
- Ash seeing the Red Genesect flying past several buildings, shattering their windows and knocking him on his ass through its speed alone.
- The Genesect Army attacking Pokémon Hills in broad daylight with Ash and co. present.
- The Genesect nest being farther up in the park, and Team Rocket falling on top of it.
- The Genesect Army attacking New Talk City itself, causing large scale destruction as civilians flee and Water-type Pokémon try to quench the ensuing blazes.
- Recycled Script:
- A lot of Mewtwo's backstory and character arc copies that of the original Mewtwo's (blowing up a lab and (maybe) killing everyone inside, going to a lake filled with indigenous Pokémon, being distrustful towards humans etc). At the end, Mewtwo even goes to a city like the original Mewtwo did.
- The series also copied the first movie's lead by directly tying in with the movie (but replacing Mewtwo with Genesect); though unlike before, the Genesect Army is only seen in a flashback and cryptically mentioned in dialogue, as opposed to Mewtwo's battle with Gary and escape from Giovanni being seen in both the movie and the series.
- Why Fandom Can't Have Nice Things: Some time after the film's release, both Hideki Sonada (the screenwriter) and Kunihiko Yuyama (the director) locked their Twitter accounts as backlash against this movie's Mewtwo rose up.
Trivia / Pokémon: Genesect and the Legend Awakened