Animation Age Ghetto: Defied for the Japanese version, according to Word of God. Takeshi Shudo states that he made the movie to entertain children and their parents/guardians as well, and that he'd be "slightly embarrassed" by parents who'd just take their children to see the movie as chaperones. It's a shame that, not only did 4Kids Entertainment dub this as a straight-up kids' film (as opposed to a family film), but many of the later movies in the series would fall squarely into this trope.
Takeshi Shudo: "Perhaps this anime is not only for children but also for their guardians: Where is this? Who am I? If you answer, 'This is a movie theater where I seldom come. I am a parent who has a child. —Ah, child rearing is an expensive, tiring job,' I'll be slightly embarrassed by your answer."
Anvilicious: Whether the film's aesop is "all life is equal" (Japanese version) or "killing/fighting (to the death) is wrong!" (English version), there's a scene with all the characters preaching about it from the sidelines. It also manages to completely overshadow the much subtler and more fitting secondary message about how one's choices matter more than one's origins, which nonetheless follows more naturally from the Japanese moral.
Ass Pull: The dub's moral of "fighting is wrong" makes sense given the context, but has very little to tie it to the rest of the movie, seemingly comes out of nowhere unlike the original's, and like Anvilicious above essentially tries to highlight "killing is bad". It also causes Mewtwo's "circumstances of one's birth" realization at the end to become this.
The Japanese original qualifies too, seeing as it has a completely different soundtrack from the dub; the movie is full of appropriate and lovingly-written orchestral music, not to mention "Mesaze Pokémon Master," the opening song. What does this version use instead of the infamous "Brother, My Brother"? An actual One-Woman Wail, which arguably gives a much better impression of the Pokémon's suffering.
The Japanese ending, Together With The Wind, sung by popular enka singer Sachiko Kobayashi (and in the beginning an unnamed little girl) is absolutely beautiful and heartwrenching.
Big-Lipped Alligator Moment: "Pikachu's Vacation" has several surreal cutaways (mostly scene transitions) to things involving other Pokémon.
Broken Base: The English dub; some have fond memories of it and still enjoy how it took a darker turn from the TV series, and even prefer it to the Japanese version for nostalgic purposes. Others dislike how watered-down and generic it was made from the Japanese version
If you watch the Japanese version, try not to hear Masachika Ichimura as Mewtwo. Lots of fans had trouble adjusting to Reiko Takashima's performance as M16's "female" Mewtwo for this reason, with Dogasunote owner of the website Dogasu's Backpack noting that he kept lapsing into reading Newtwo's dialogue in Ichimura's voice when going through the M16 manga adaptation. When Mewtwo returned as DLC in the latest Smash Bros. game, Keiji Fujiwara's take on it was clearly inspired by Ichimura's performance.
For the English version, this can either be subverted or played straight depending on your point of view, in that both Philip Bartlett and Dan Green (who took over the role in Mewtwo Returns) seem to be equally well-remembered as Mewtwo's voice.
Critical Dissonance: Did poorly with critics, but ended up being the highest grossing anime film released in the United States. Modern Pokémon fans also have a somewhat higher opinion of the movie, where it is considered polarizing instead of universally bad. However, the Japanese version is usually considered outright good.
Critical Research Failure: Courtesy of the English dub; in one scene Corey refers to his Pidgeot as Pidgeotto, and in the scenes of Mewtwo's lab Team Rocket mistake the silhouette for Scyther as Alakazam.
Draco in Leather Pants: Interestingly enough, both Mewtwo and Mew get this treatment, as the latter is much less innocent in the Japanese version than in the dub:
In the Japanese version, Mew is an even bigger victim of this, especially to people who grew up with the English dub. While it does side with Ash, it believes the originals to be superior to the clones and wants the clones to lose in a fight to the death. The problem is, due to Mew being a Ridiculously Cute Critter and much less menacing than its clone, and the fact that Mewtwo is quite a dick and its clones serve under it, people are inclined to side with Mew despite the movie's moral of "all life is equal."
Ear Worm: "Vacation" by Vitamin C. Good luck getting it out of your head.
Evil Is Cool: It's often agreed that Mewtwo is the best antagonist of all the Pokémon movies, with its immense power, Badass Baritone, cool design, being an actual villainous Pokémon and having darker objectives compared to the other movie villains.
Fanfic Fuel: Exactly how Mewtwo kidnapped Nurse Joy is left unexplained. Did it find her himself, hypnotize her and take her back to its island? Did Mewtwo have a different Pokémon abduct her and then hypnotize her? Where did it get her new outfit from?
Most people know there were at least two movies, but most people (at least outside of Japan) don't know that there is an nineteenth movie, and counting.
Overlapping with the above Cant Unhear It, this version of Mewtwo is by far the most remembered iteration of the character to date. In its appearances in the Super Smash Bros. games, its overall portrayal is based on this specific one.
Franchise Original Sin: Though it's rather downplayed (and excised completely in the English dub), Mewtwo is Not Evil, Just Misunderstood, and merely seeking a purpose in life (if going about it in completely the wrong way). Later Pokémon films with actual sinister-looking Pokémon as the (apparent or actual) Big Bad would go overboard with this trope, to the point where such a Pokémon either not being evil or making a Heel–Face Turn is a common and tired cliché they share.
Growing the Beard: Specifically in Japanese, as the movie was one of the first Pokémon products to implement complex ideas and themes that would give older viewers something to appreciate and think about, only beaten out by some early manga or the occasional in-game moment that touched on these (or in the case of Pokémon Adventures, took them and gleefully ran with them over the horizon), with the wider appeal of the anime leaving a heavier impact. While the English dub was much more simplistic, it at least kept the dark tone of the original, and many people still regard it as a step up from the regular episodes.
Because Mewtwo's special Poké Ball wasn't given an actual name in the movie itself, some have actually started calling it a Master Ball because of the "ridiculous" catch rate. A later episode would feature an actual Master Ball, and it failed in capturing a Pokémon (a Whiscash).
A genetically modified, terrifyingly intelligent, all-powerful monster with a primarily white color scheme and an intense hatred for humanity due to being mistreated by its creators? Mewtwo is essentially a redeemable version of the Indominus rex.
From the soundtrack, a few of the songs become easily applicable to events in Pokemon's future, as opposed to being completely unrelated to anything in the film. For instance, "Making My Way (Anyway That I Can)", a song about overcoming hardships with newfound courage and strength can easily be seen as Lillie's theme song.
Jerkass Woobie: Mewtwo; while there's no denying that it's a dick, it had an incredibly tragic life up to the point where it vowed revenge on humanity. Even more so in the Japanese dub, where it just wants to prove itself worthy of its own existence.
Magnificent Bastard: Mewtwo, pre-Heel–Face Turn, fits this to a tee. Brilliant? Check. Smooth operator who almost never loses its cool? Check. Has a goal and is going to get there, dangit? Check. Charismatic? From the high amount of fans it's earned, it seems safe to say check. Savvy? Pretty much so. Audacious? It doesn't get much more audacious than trying to wipe out all life on Earth.
Memetic Mutation: "Pokémon aren't meant to fight. Not like this!" note Due to being released in America during the height of the "Pokémon is Animal Abuse" controversy, 4Kids decided to take it upon themselves to insert an anti-fighting aesop into the movie.
Narm: A few examples, mostly thanks to the changes 4Kids made to the original film:
4Kids' editing and script changing is a source of this, though there seem to be just as many people seeing their work as Narm Charm instead.
During the sad scene where all of the Pokémon are crying over Ash's body, the Dewgong start making sounds that are downright hilarious, especially in the Japanese version. Mood Whiplash at its finest.
Some people, critical of the English dub, find the "Brother My Brother" song to be a case of Soundtrack Dissonance.
The Harbor Master's Info Dump on the prophecy of a "great storm", supposedly the one being created by Mewtwo. Aside from being blatant exposition on what's to come, many may be tempted to believe she isn't all there reciting this bizarre story to them.
Team Rocket's viking disguises, which has to be one of their least credible, treats us to this quip from Ash that "They mostly live in Minnesota".
Misty's response to Mewtwo's evil plan? "You're just a bully!"
The entire message about how fighting is wrong is made of this, which countless fans have mocked for it being completely out of place in the series. It does not help that the English dub tries so hard to force it into the audience's heads.
Narm Charm: Similar to The Transformers: The Movie, a lot of people enjoy the English dub due to nostalgia, the pop soundtrack, and Mewtwo's badassery as a villain, despite everyone acknowledging that the movie isn't one of the best around (as evidenced by its very, very low Rotten Tomatoes rating).
Subbing vs. Dubbing: The dub is far more well-known in the Western fandom, and quite a few fans even ignore that the Japanese version exists. Despite this, people who can find the Japanese version tend to prefer it (thanks, Shudo).
Vindicated by History: To some extent. The movie used to be on the IMDb Bottom 100 when it debuted, but now sits at an average rating. Most of the votes were initially from disgruntled adults taking their kids to see the movie, but they later became dominated by grown Pokéfans. Easier (but not outright "easy") access to the original Japanese version of the movie also helped, as it motivated quite a few Pokémon fans who aren't too fond of 4Kids' dub to revisit the movie and develop a more positive opinion.