Best Pokemon Movie(s)? | Bulbagarden
The movie does a great job advertising the legendary Pokémon while also giving the human characters focus. The Japanese version with the Birth of Mewtwo is very sad especially since Mewtwo's and Fuji's backstories are expanded upon in the CD drama. It sucks that it doesn't seem to be canon anymore since the remake excluded these scenes even in the Japanese release.
I wish Musashi would have been more relevant since Miyamoto's plot revolves so much around Mew. Kind of strange that we never found out what happened to her.
I also wish Ai would have been more relevant even if she might be dead. It's a shame that she only gets a vague reference in The Return of Mewtwo when Mewtwo watches the sunset.
2. Emperor of The Crystal Tower: Entei
This movie also has very good human drama while still advertising the new Pokémon. Molly is a very sad character but I don't like how her parents magically comes back to life at the end. It makes the movie a little bit unrealistic since it's was otherwise a good portrayal of grief (denial, anger, depression). Molly goes through the various stages of grief but instead of overcoming it and moving on, the situation magically resolves itself.
Satoshi also has a good motivation to fight Molly. Hanako is actually a great character after reading about her backstory in Shudo's light novel so I'm glad she got some actual focus.
I also like how Kasumi, Takeshi and Charizard helped out. Even if they usually get demoted to background characters this movie showed that they were willing to put themselves in danger for Satoshi's sake.
3. Mew and the Aura Hero: Lucario
I like how it manages to give Lucario an actual character arc and how it doesn't hyper-focus on legendary Pokémon. The scene where Lucario fades away is kind of sad since he was somewhat of a well-rounded character if you compare with Latios. There are also some interesting themes such as betrayal and trust.
I also liked the scene when the characters get swallowed by the goo and think they are going to die so they release their Pokémon in a desperate attempt to save them. Normally I don't like all these fake death scenes in Pokémon movies but this one was actually great because it showed how much they truly cared about their Pokémon.