We've been so deadened as a society that we think that that is "cheesy," and "children's material." No. As an adult, I understand why that was so heartbreaking: Because that's the way many people in the world are, just fighting each other to prove that their purpose means anything, instead of just banding together in friendship.
The most saddening part of the movie as a child was when Pikachu just kept taking the hits without retaliating. Pikachu's will is so similar to that of Ash's that he refuses to fight the other Pikachu (essentially, refuses to fight another living being to prove to the other Pikachu that the fighting is pointless - even Meowth, who's supposed to be one of the "bad guys" knows better than to fight like that), even as it continues to slap him over and over again. The relationship between Ash and Pikachu is the entire central theme of Pokémon: friendship prevails over selfishness. Pikachu is the Pokémon embodiment of friendship. The reality of friendship "slaps him in the face" as he sees all the Pokémon weeping over the petrification of a human being who only wanted to protect his friends. Mewtwo makes his own purpose in life the destruction of life itself, but realizes that isn't the way things are supposed to be. Pokémon and their trainers can be friends, but can also walk their own paths, just like all humans in real life. He eliminates the antipathy between humans and Pokémon by realizing that they're all the same. Mew loves mankind because he knows that they're just another form of life on the planet. Mew is his foil, as Mew is everything that Mewtwo is, minus the hatred. He has no purpose of his own, he didn't know he was, so he lashed out against all of humanity, and against the Pokémon he felt were being used by their masters. Treated as less-than-life - a tool to be used for human purposes, rather than a living being with a living will and a purpose. Mewtwo's hatred for mankind stems from their lack of compassion - he was basically used.
The whole series is an allegory on how you're supposed to treat your fellow man, using the relationship between Pokémon and their trainers as a parallel for the relationship between human beings.
The reason why Ash is always able to win is because he's friends with his Pokémon. This was my favorite movie as a child, and it always made me sad to watch it every time, so watching it again having gone through the self-discovery of adolescence made me realize why it was so impacting. If they fail, Mewtwo’s vengeance will not only lead to tyranny over all the Pokemon, but also the extinction of the human race. United together, human and Pokémon alike, they must not only discover the hidden secret of Mewtwo's plans, but stand against his terrifying might. Among these trainers are Ash Ketchum, his loyal Pokémon Pikachu, and their friends Brock and Misty. Under the guise of being a master Pokémon trainer, Mewtwo lures the best trainers in the world to his base.
Breaking free of his control, Mewtwo creates his own island fortress and reconstructs the cloning technology that gave life to him. Pokemon: Mewtwo no Gyakushuu reveals the terrifying power of Mewtwo as he learns that not only was he created to be an experiment, but also to be a tool for Giovanni’s sinister dealings. With advanced cloning techniques and resources provided to them by Team Rocket crime syndicate leader Giovanni, the scientists succeed in creating the powerful psychic Pokémon, Mewtwo. When a team of scientists discovers the DNA of the ancient Pokémon Mew, they harnessed the potential within it in an attempt to create the ultimate living weapon. It was a successful science experiment gone horribly wrong.