Here is what I want this game's story to live up to. XD Though it's a long shot...
There is no evil group, only evil Pokemon. When you first start, everything is like a normal Pokemon game. But as you travel, you see news of disasters, and Pokemon going insane, attacking people. Two Pokemon (A "light and "dark" Pokemon) Are feuding between worlds, a "light side" and "dark side". You as the protagonist must travel between the two worlds and calm the two. But on the other side, there is another you, who is an opposite. You are your own rival. The Pokemon in each side are different, as are the trainers, but the areas remains the same. This give the game longevity, as you have two different areas to fight within the one region. This could be why the first town is so bright, but the city is dark. They are on different sides of the spectrum.
I'm just rambling off of the top of my head, but this is my almost ideal Pokemon plot line.