The montage of Mewtwo's training, watching some of the most powerful Pokemon get their butts handed to them was pretty sweet.
If you need more convincing, want to know one of the people he managed to defeat in seconds? GARY FREAKIN' OAK!
Mewtwo's Badass Boast at the end of the intro, particularly in Japanese, with this version often being quoted by our friends on the other side of the pond.
I curse everything I was born upon. But this is neither an attack nor a declaration of war...! Against all of you who brought me into this world, I will...strike back.
Mewtwo and Mew's battle royale was also totally wicked.
Mew's entrance was especially awesome because not only was she the first one to even touch Mewtwo, she slammed him through the floor!
If you're attentive, you can hear Mewtwo shout in pained shock as Mew's attack plows into him. He totally wasn't expecting his progenitor to be capable of even scratching him, especially after he'd just seemingly blasted her into space (complete with shocked "MEW!" of pain). It's the only time in the movie that anyone catches him with his proverbial pants down.
Charizard VS Charizard! Let's be honest Ash's Charizard, despite always being called weak/poorly trained is the only one of the three that put up a real fight. He still got curbstomped though...
Ash addresses a Legendary Pokémon and its army of genetically enhanced clones (while striding out of smoke with the originals in tow): "You can't do this. I won't let you." Mewtwo and his genetically engineered super-Pokemon were balanced by Ash Ketchum's gigantic balls.
It was recognized by Toonami for being awesome, too.
He then proceeds to try and run up and punch Mewtwo in the face! When he's knocked to the ground, Ash gets up and does it again, this time getting thrown ass over tea kettle for his trouble. Ineffective though his attacks may have been, the sheer display of guts has to qualify as a CMOA.
Ash: "He can't capture our Pokemon if they're already in their Pokeballs". Mewtwo: (Does just that).
Keep in mind that this is also the only way they were captured. Before that, Bulbasaur and Squirtle were the only ones who were actually holding their own against Mewtwo's Pokeballs.
To add to the awesome, Mewtwo, IIRC, is actually smiling right before he captures said Pokéballs. It's not his only smile in the movie, but it's certainly his best timed.
This is followed by the Poké Balls chasing Pikachu up a spire, Pikachu shocking them repeatedly, and swarming it until they drive the exhausted Pikachu to the spire's peak. Then they knock Pikachu off and capture it in free-fall.
Mewtwo throws around a lot of Pokemon and people alike with his psychic powers, which makes the time offhandedly he catches a charging Rhyhorn by the horn that much cooler.
Mewtwo casually catching a Hyper Beam which is considered one of The most Powerful Moves a Pokemon can learn and throwing it back at Gyarados knocking it out.
When Giovanni firmly grasps the Idiot Ball and tells Mewtwo that his sole purpose is to serve humans. Mewtwo's reply is to blow up the entire building.
Mewtwo's perfected cloning machine, as shown in the scene with Team Rocket. Explosions? No big deal. A Pokémon less than a year old perfecting a cloning technique to make clones instantaneously, when the scientists who created him from that technique only had one surviving subject out of at least five, and only that due to how tough Mewtwo is as a legendary Pokémon? Crowning moment of brilliance as well as awesome.