Third idea, but since I'm getting back into the spirit, I might as well say what I have. It's more basic then the other two, but since I'm pretty much starting out, I wouldn't be able to do it yet. And it is a prequel to the second idea.
In the region of Altoria, before the corruption, before the Licentia, and before the region was split into two, there was a Pokemon League. It was successful, and brought in a bunch of trainers. You are a trainer that will go on a journey in the region, but you will be one of the last as well.
In the shadows, a team known as Team Enel existed, ateam that threatens the peace in Southern Altoria, as well as the balance of the world itself. This team's goal: To summon Jirachi to wish that every last pokemon did not exist. Now, if this were to happen, then life itself would die off, but most of the team never thinks of that fact, due to their ignorance and stupidity. The leader knows this all too well, and still goes after it.
Then the jail break occurred, allowing some of the most dangerous criminals free. These dangerous criminals also threaten the peace, and they often war with Team Enel. Their goal? To do what they want. They have no formal name to one another, but to everyone else, they're known as the Legion. The reason for their alliance is so that they wouldn't get overpowered by the police.
With the insane, hypocritical team, and desperate, power-hungry criminals, will you be able to last in the region? Can you become the Champion of the region? Well, the second question I can answer, and that is a big NO. You'll find out why later on, but it should be pretty obvious.