A Pokémon game where you have to fight a dictator that despises Pokémon being used for battles, he think they should be used for work Humans don't want to do, friendships and trust can't be made with Pokémon etc.
But really, I think a Pokémon game where you start a world where Pokémon battles are outlawed, and any trainers found will be sent to jail because of the Dictator that hasn't been taken out of Power.
I mean wouldn't it be awesome for you to start a rebellion and try to get loads of people to help you when you finally attack at once, in a sort of Fable 3 manner, acquiring people to take down the king.
Instead of getting 8 badges through Gym leaders to beat the elite four, you have to go to each city, and find it's ex-gym leader, and get their trust, you have to find an underground resistance in each town/city, and enter it. Upon doing so, it acts like a gym, to see if you are worthy and tough for them to help, once you beat them, they give you their old badge, as a sign they'll help you.
And possibly half way through you get captured and you talk to the Dictator face to face, but you soon escape.
Then right at the end, once you storm through his guards and finally get to him he tells you this.
"You, "Player name" you think you can stop me? I've been a successful ruler of this land for longer than you were born and I'm not letting a 10 year old take me out of my position for nothing, but you want to know something funny, I may outlaw Pokémon battles for you, but I don't, I train my Pokémon all the time. Not only that, I assembled teams that would beat any Pokémon type! Do you know what that means? I'll tell you! I am the most powerful Trainer in the world!"
And then this music plays. (or a variation)
http://www.youtube.com/watch?v=Pjs3UfjRLec
I know it's not really thought out and developed, but it's basically the main idea.