Well yeah, your all correct about those being dark things.

but calling pokemon dark because of those parts is a bit like calling a day in the middle of summer a form of "night" just because it has a shady tree. sure its less bright because of it, but its not exactly something that sets the overall atmosphere because your still enjoying a sunny day outside with your excitable dog. especially if they are presented in ways that you need to think about it to really get how dark it is? you can pull darkness out of a lot of things if look hard enough because focusing on that is more of a mindset than anything else.

when really when pokemon as presented in its full context? shows a world of people working together in peace and having a good time with war being seemingly a thing of the past and the only strife coming from stupid criminal gangs with weird goals, with most people having nothing better to do than to compete in various pokemon competitions, and the pokemon being completely okay with this for the most part and living and cooperating with humanity in harmony. which still hasn't changed since Gen 1. so personally I wouldn't miss the sunny day for looking at the shady trees.