This is interesting. How about a concept where YOU are Team Rocket/Magma/Aqua/Galactic/Plasma? An idea like this has always interested me, where you are the bad guy. You would have to perform missions for your boss, and if you did well, you would receive better Pokemon. You could also be promoted from Grunt to Commander to Admin, and receive other prizes along the way (items, badges, etc.) to show how good you are. Hell, there could even be ONLINE where you join groups and go out into squads to perform a multi-mission! That would be epic!
What would the missions be about? Stuff like...
~Having to defeat and take Pokemon from other trainers
~Having to steal precious items from museums and such
~Finding information about a secretive topic
~Stopping other Trainers from infiltrating your base
~Beating other Grunts/Commanders/Admins to gain higher rank
~Finding new Pokemon/items for your Team
~Coming up with new plans to TAKE OVER THE WORLD
...you liek?