>>49553660The Pokemon series as a whole runs on fighting game logic, characters letting their "fist do the talking" aka Pokemon battles, using that as a way to understand one another, it can be assumed Pokemon caught simply view you as the stronger person and respect you, which is why they follow you after capture without question.
This also explains why they don't listen to trainers that they're traded too, as now they're with a person they don't know is worth their time to follow, as they get badges it can be assumed their skill as a trainer grows to the point where Pokemon notice and don't question this new person.