In the case of these stories, I think people are indeed overreacting because they are supposed to be the equivalent of real life folk tales, where it's not uncommon to anthropomorphize animals (e.g. swan maiden, sirens...).
However, I think Pokémon in general as a franchise always had a certain element of sexual titillation from the beginning, especially in the original Japanese versions. Nowadays it's more sanitized, but just to give some examples:
- In the first anime opening, one of the first lines is about a girl's skirt.
- Misty and her sisters are described as extraordinarily beautiful girls that captivate men.
- Many female characters have suggestive designs.
- Celadon Gym is full of beautiful girls to the point there are men who go there just to look at them.
You only think Pokemon is "pure" because you were a child and experienced a somewhat more sanitized localized version, but if you started watching the first Pokemon anime in Japanese today, you would definitely notice it has elements that sexually appeal to young boys, the original audience. The Pokemon world being full of young attractive girls makes the adventure more appealing. And now we have even more proof that this was the case, with those design documents describing sexy gym leaders.
There are very few "pure" franchises, apart from those aimed at children. Almost everything tries to sexually appeal to some group with things that they feel attracted to. I'd bet many asexual people probably follow the same patterns too (for example, asexual women might like media that depicts attractive men). In the end, humans are horny animals, expecting people to act in a "higher" sense will lead to disappointment.
