I suddenly remember a theory that the pokedex entries themselves are like Ripley's facts in order to encourage users (Children) to collect more while it really harvest complex biometric and genetic information. As such, they really shouldn't be trusted.
Oh, and I think the original super-dark theory was that Gary's Raticate died as a result of the SS Anne battle.
Edit - In response to Razier, I think if there is an actual thematic, consistent darkness is that for all of the things that give people hope and a reason to live there is a dark shadow. It shows up in Magma and Aqua wanting to ensure the resources for future generations to live to the pursuit of knowledge itself creating existential threats in X and Y.