The idea seems interesting, but I do have some questions:
#1. How will you into this? I can see the main character being some new addition to Team Unity, or even a commoner who idolizes the Team at first, but then realizes their motives cover gruesome behavior.
#2. Gyms. Pretty basic question. How will they fit into this? Will the Leaders be associated with Team Unity, or will they lead some form of rebel union?
#3. Ancient long-gone Pokemon? Cliche, to say the least. If it's a Fakemon, even worse. Elaborate?