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I think adult incompetence must play a role. Team rocket grunts act like bumbling morons, dropping vital keucards and divulging important info. Their victims are even dumber. In the Pokemon world most adults leave their front door unlocked even though burglars/arsonists and ninjas exist, not to mention thieving Pokemon.
Based on how stupid some of the Pokedex entries are, and the fact that she doesnt have any education beyond elementary school, the protag isn't a genius herself, so the average Pokeworld inhabitant must have the intelligence of an infant to be outsmarted by the protag, which explains why their entire society revolves around monster fighting.