The games certainly have a different atmosphere than the rest of the series. They don't have that same sense of adventure as in the main series games, but instead have that sense of danger reminiscent of Majora's Mask(with the Moon and whatnot). The Shadow Pokemon attacking their own trainers seems hostile in and of itself, but when we have an organization that has the ability to infiltrate into Politics, Industry, Architecture, and BioEngineering to achieve their goal, and using a Team Rocket -esque proxy to do their dirty work, then, you have danger. The Majora's Mask(s) of Pokemon?