Mmmm, well. I haven't put much thought into the plot or designing the game board. I'm thinking that I'm gonna make Team Rocket really cool, and actually well trained. They used to be really lame and weak, something you'd take on for breakfast.
Moreover, the plot has something to do with some weird internet thing. I'm thinking everything is going to be made of data. The player would connect to the net using some kind of port, and then is transported into the world of pokemon. Maybe the world is post apocalyptic or something. When you "talk" to the TV, you get transported to the real world, which is a lame place to be in.
Like I said, I've got a lot of ideas in my head. None of these are final, but they're all good ideas.