- Anvilicious: The movie's largely disliked Green Aesop.
- Badass Decay: Mewtwo, until the ending that is.
- Critical Research Failure: At one point, a father Rhyhorn and mother Nidoqueen are seen with their children of both species. In the games, Nidoqueen can't breed, but maybe they can in the anime, similarly to Legendaries. What can't be handwaved, however, is that they've given birth to baby Nidoqueen. Not baby Nidoran, Nidoqueen. As in a third-stage Pokémon. A third-stage baby.
- Ensemble Dark Horse: Domino, a girl with a little over seven minutes of screentime, and around a quarter million words of fanfiction. How can you not be when you get to wear opera gloves and thigh-high boots all day for a living, and have a cute hairstyle and a Nice Hat?
- Evil Is Sexy: Domino and (let's face it) Giovanni (not helped by the below-mentioned Foe Yay between him and Mewtwo.)
- Foe Yay: Quite a lot of the dialogue between Mewtwo and Giovanni is bizarrely sexual, including Giovanni telling Mewtwo he is a 'good boy' and that now Mewtwo won't be able to 'run away from him again'. Mewtwo also asserts that he 'will NOT submit!' when he is being tortured by Team Rocket's machines.
- Memetic Mutation: When it starts raining, "I'll use my trusty frying pan... as a drying pan!" from Brock.
- Nightmare Fuel: Mewtwo's effort to break out of the torture machines. Seriously, what the hell was that?
- Paranoia Fuel: When questioned by Calix when she revealed her true colors, Domino confirmed that she indeed was in the Pokémon Institute...and also implied that Team Rocket has agents everywhere.
- Tear Jerker: Mewtwo surrendering himself to Giovanni.
- They Wasted a Perfectly Good Plot:
- Mewtwo's aforementioned Moment of Awesome isn't even shown, occurring offscreen.
- This marks the first time Ash and co. have actually met with Giovanni, but nothing is made of the issue.
- Wangst: Mewtwo has this, until he gets over it and has a Moment of Awesome in the end.
YMMV / Pokémon: Mewtwo Returns