Mewtwo vs. Mew is not only my favorite Pokemon film, it's my favorite film period. As a Pokemon nut I love it, but that's not the only reason. It teaches excellent themes, like the value and uniqueness of each life, the value of friendship, and how horrible fighting is. A person on another forum I visit once said that the war in Mewtwo's battle field is a metaphor of wars like WW2. War and fighting are terrible things and the film illustrates that well. It isn't until a life is lost (Satoshi) that the Pokemon come to their senses. And there's my favorite movie scene ever. It's also the only scene in a movie that always makes me cry. Think about the concept. The Pokemon realize what they have done wrong and they mourn for the life lost. Pikachu is especially upset, having just lost his best friend and life-long companion. But when the Pokemon cry for Satoshi, their tears bring him back (I always see this as God heard their cries of sorrow and restored Satoshi, hence the great light shining down around him). Then Mewtwo finally realizes the bond between a Pokemon and its trainer. And there's my favorite movie line ever.
"The human sacrificed himself to save the Pokemon. I pitted myself against them. But not until they set aside their differences did I see the true power that they all share deep inside. I see now that the circumstances of one's birth are irrelevant. It is what you do with the gift of life, that determines who you are."
This movie is just incredible. That's the best way I can probably describe it. It's a very entertaining, and emotionally moving film.