My part 3 comes from your critique of that essay. So basically in your responses I gathered, you believe that the trainer and pokemon relationship has both equal and unequal characteristics. Do you also think that certain types of pokemon have more of a subservient attitude towards humans?

That seems unavoidable to me.  Some Pokémon are very used to teamwork and cooperation in nature, like Mightyena or Beedrill.  Taking orders in service to a larger goal just makes sense to them.  Other Pokémon are inherently very individualistic, like Charizard, or used to manipulating others, like Malamar.  That doesn’t necessarily mean they dislike humans, but they might be more likely to come to that relationship from the perspective that they know better than you do, or be more concerned with making sure they’re getting something specific in return for their help.