I really don't see how it's that appalling that humans are the cause of the world's turmoils. It's truth. If Man did not exist, or at least existed in a much smaller number, than a majority of the issues effecting the world would be entirely non-existent (Pollution, extinction, global warming, to name a few).
The same goes for the world of Pokemon. Take the species of Grimer. It was born from gamma radiation to toxic sludge. Where did that sludge come from? Human facilities. Now, I'm not saying that Grimer is a bad Pokemon, but it's just an example. If you look at each game, there are subtle examples, and very apparent ones, of humans being the cause of pain for Pokemon and the environment at large. Team Rocket in R/B/G/Y/G/S/C alone caused hundreds of Pokemon pain by forcing them to be subjects to cruel experiments (The Radio Tower scandal in Mahogany).
Also, the manga (Pokemon Adventures/Special) clearly brings to light the suffering Pokemon endure under cruel Trainers and selfish humans. In fact, the entire Yellow arc of the series is centered around Lance's extremist views to eradicate humans as a result of watching the effects of pollution in Kanto.