Also, can I just throw in that people should stop referencing Genesect's appearance in the movie? I mean seriously, not only is Mewtwo the bigger character more people are interested in, but it's, by far, the WORST legendary/unique pokemon star in a movie. I mean seriously, it's been all over the place for Pokemon Movies.
Mewtwo: Badass who wanted to destroy the world, and the first time we ever saw people DIE in Pokemon.
Lugia: A strong leader character who, while was not very talkative, let its actions speak for itself. Not to mention his speech is VERY inspiring.
Entei & The Unknown: The whole tale of the third movie overall is very sad and depressing, and this movie's main characters strike the second most home IMO. She just wanted a family to be with ever since her father disappeared, she never wanted harm to come to anyone, but the Unknown's power was too much for her young mind. So damned if I say that these characters, especially Entei, are really well done.
Celebi: Average at most. I did feel for Celebi in its dying moments, but the villain felt incredibly bland as well as his overall goal. He wasn't smart like Mewtwo, he was just a mindless brute. Celebi's not the best, but not the worst.
Latios & Latias: Latios and Latias are my second favorite movie characters, and the sacrifice that Latios makes in this movie is very noble, even possibly aware of his own demise. Yes, this is the first time we really see a main character DIE in a pokemon movie, and it was very sad. I will remember Latios, and I hope you will too.
Jirachi: This character was, in my opinion, the SECOND weakest main star in a pokemon movie. Maybe it was because the movie focused mostly on Max, but it was just so bad. Also, Tentacle Hentai Groudon is enough to give you nightmares.
Deoxys: It takes FOREVER for this movie to get going, but you can get to feel for Deoxys in the end. However, the story of this movie is overall pointless and rather boring, which really brings down Deoxys' character.
Lucario: Lucario was noble and strong-willed, giving his life to save the world. He was a good movie star, but not THE best.
Darkrai: As someone who had a terrible childhood revolving around bullying and being shunned for no other reason than being different, I can feel ALOT of sympathy for Darkrai's character, and his sacrifice for the people that shunned and hated him was something that was really touching. Darkrai is one of the better movie leads.
Giratina and Shaymin: I didn't care much for Shaymin, but seeing how the Distortion World worked was really cool seeing as Giratina is my favorite pokemon. However, the villain sucked in this movie and really brought down the movie in the end.
Arceus: The God of all pokemon is a sniveling crybaby who throws temper-tantrums and sounds like Sonic the Hedgehog with a stuffed nose, which is kind of funny seeing as the villain sounded like Shadow. Anyways, the only good parts of this movie are the fights between The Legendary Sinnoh Trio and Arceus.
Zoroark: My favorite pokemon lead, and for good reasons. This movie wasn't trying to go over the top of saving the world like the past movies had kept throwing out over and over again, and Zoroark wasn't even a legendary pokemon, she was a poor pokemon being forced to do evil, all for the sake of her own baby. Zoroark went through endless amounts of torture and ill-treatment throughout the movie, and it was all so that she could be reunited with her baby Zorua. Hell, she gives all she has to protect her child that she DIES, SHE DIES. She doesn't die for the world, she didn't die for the fate of the universe, she died for the safety of her own child, and in my opinion...that's the most noble death in the series. Sure she was brought back to life by Celebi, but Zoroark really leaves an impact.
Victini: Victini's story is sad, and you can feel for the character throughout the movie. However, agan, the villain sucks and the plot is almost completely unnecessary. Not a terrible movie, but not good either.
Keldeo & Kyurem: Listening to a great VA keep on whining is painful, but the best part of this movie is the fact that it's the best voice-actor wise. The only other good thing is Kyurem's appearances and almost chilling voice, but the rest of the movie is just "RUN IN CIRCLE BACK TO WHERE IT ALL STARTED!"
Genesect: Genesect sucked. It was a weak villain with a weak goal and a SUPER EARLY RESOLVE. Mewtwo was a great character, but was sadly brought down by Genesect.