The montage of Mewtwo's training, watching some of the most powerful Pokemon get their butts handed to them was pretty sweet, in a terrifying sense.
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.
Ash's battle in the opening scene, starting with Bulbasaur taking two Rollouts from Donphan and getting up like it was a light attack, then blasting Donphan with Solarbeam. Double points for this being Donphan's first appearance before Gen II.
Squirtle's Curb-Stomp Battle against a Machamp... who goes down from one usage of Bubble.
Following the above, the opposing trainer, frustrated that Ash's Pokémon so far downed his in one move each, sends all of his remaining Pokémon at once, which are a Pinsir, a Venomoth and a Golem. Cue Pikachu leaping from Ash's shoulder and unleashing a massive Thunderbolt that KO's all 3 of them, including the Golem that, by all accounts, is a No Sell to Pikachu's attacks.
For extra points, both the English and Japanese versions accompanied by a remix of the original title theme of both their respective series dubs.
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.
Also, the fact that Mewtwo can go head-to-head with Mew while also blocking the elemental powers of about four dozen Pokemon further shows how freakin' strong he is.
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...
when Ash first calls out Charizard, he immediately locks on to Mewtwo and blasts him with a Flamethrower. It knows a challenge when it sees it, and didn't hesitate to attack. Too bad it didn't do anything.
Ash addresses Mewtwo's 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).
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.
It doesn't end here. Ash, seeing that Pikachu was captured, jumps after the pokeball that holds him and follows it down to the cloning device. Despite struggling against dozens of mechanical arms, Ash struggles hard, ripping off a few and visibly trying to chew through one. He by no means makes it out easily, but he gets Pikachu out anyway through sheer willpower - his efforts rip apart the innards of Mewtwo's cloning machine (complete with chain reaction), freeing all the captured pokémon in the process.
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.
Team Rocket somehow managed to stop a flying Dragonite with a pan.
Also, they were successfully braving the storm with a small boat. Had they not stopped driving it to recite their motto, they could have arrived to New Island with it.
On a minor one, it's implied they didn't get invited to new island, which is an awesome jab by Mewtwo since he used to work for Team Rocket.
A subtle one, but Giovanni just confidently walking up to something he's seen effortlessly destroy an island.
While it's a Tear Jerker, Pikachu's fight with his clone is awesome as well. Not only does he refuse to fight a pointless battle, but he stands his ground without fighting back against someone more powerful than him and let him wail on him till he collapsed while the others we mostly getting curbstomped despite fighting back. Balls of Steel. Is there any doubt now that Ash's Pikachu is one of, if not the most badass Pokemon to ever exist?
Pikachu's resistance is so great that its clone looks even more exhausted than it does despite refusing to fight.
Meowth's clone is the first clone to refuse to fight, unlike Pikachu's clone that beats Pikachu up until it collapses.