Pokemon Movie 01: Mewtwo no Gyakushuu

Dian from Jewelpet is basically like Mewtwo: Both are psychic mage cats who rebelled against humanity for the sake of their kind before being redeemed by the power of friendship. 

If you liked the deep themes of the first Pokémon movie but you want to go far, you should definitely try Neon Genesis Evangelion. In my opinion the first Pokémon movie took inspiration from this anime, they both share themes like clonation, recreation of life, biological issues... I really wished all the recent Pokémon films were inspired by this great anime era and had some meaningful story inside them like the earlier ones. 

Both are tales of innocent creatures of abnormal birth having their hearts darkened by mistreatment. However, while Mewtwo Strikes Back is a kid-friendly tale with a happy ending, Elfen Lied is a gorefest that may not be safe for some ADULTS. 

Both the first movies in iconic kids Anime franchises; Pokemon & Beyblade. Both see our heroes in battles with increased stakes than our usual battles in the respective TV anime series. Both could be considered defining moments for the main characters.