Sounds very intresting. I guess you are still planning. So is there more than one villian in the story? It seems that you implied that Deoxys is controlled by another entity. People might get weird over Crystal Region, so perhaps the Crystallia Region instead? :D
Oh and since this is a terriorist groups, having conflicting conflicts over if the terriorist group is "good" for fighting for Crystallia or "bad" because they are looked down by the government and the evil man? Have you seen Psychopaths? It's an anime with similar stipulations on morality. I'd definetly watch that for inspriation.
Nice idea you got going there, I love it :D