I think the pokedex entries can be used in the deconstruction, if just because the science behind them is so awful; 5000 or whatever is not a possible IQ score, Steelix is less dense than water, Magcargo is hotter than the sun, etc. All the science in pokemon seems as if it was written by laypeople with little to no thought or interest in its accuracy.
I'm not saying the world is necessarily theocratic, but it does seem anti-intellectual in spite of all the impossible fantasy tech. It sorta reminds me of americans enjoying western medicine while fighting against the teaching of evolution in schools. Obvious some people know what they're doing, given the invention of Mewtwo / resurrection of fossil pokemon, and the fact that all this tech needs to be maintained by someone. Bill has a teleportation machine, but considering that pokemon and items (in RBY) are able to be stored on a computer from the onset of the game diminishes his achievement a bit, I think.
But I don't give the pokemon researchers a lot of credit. I like the idea that "genderless" pokemon are actually just cryptic, and this explains things like starmie (starfish do have sexes, but could a hack like Oak really tell between them?). Fungus (and in the case of Cradily, an animal) gets classified as "grass" although Fungi are sister to Animalia and therefore more animal-like than plant-like. Basically, biological classification in pokemon, at least as evidenced by the pokedex, is done by amateurs and laypeople. I like the idea that the "pokemon journey" is a ruse to get you out of the house while your given region's pokemon prof works on scrogging your mom, because it makes way more sense to me than "all the biologists of this world are hilariously inept."
When do we even see scientists in RBY? They work for Team Rocket, right? So, and maybe I'm stretching things here, science itself could be criminal in the pokemon world. That's just an idea I like, don't know if anyone thinks its worth using.
That was kind of long, there's a lot I wanted to say about the systematics / hierarchy of life in the pokemon world and the idea of exploding pokemon being akin to eusocial insect warriors dying to preserve their colonies, and therefore their genes. But this is my first ever post and I don't want it to go on forever.