At the beginning I had the same idea to use a specialty ball to use for capturing Shadow Pokemon, my thoughts were the Dusk Ball or Dark Ball (4ever). If I do plan to use that concept, I want to make custom villainous-type ball (Rocket/Magma/Aqua: Used in TCG/Anime) that would snag Pokemon. Team Static and Serial INC could of easily manifested such an item.
Also just updated the Features page with this information about Shadow Pokemon and a cool new idea...see spoiler:
Fire Flyy, I know it is a lot... but I dream big. I had the same idea to only include the Serene region, but I want to see how far RPG Maker XP can go without falling apart. It will be a risk I will take along the way.. Thanks for the comment though! I really appreciate the feedback, guys.