They want stories where the villain is catching pokemon, but if they're just catching pokemon the same way the heroes do it it'll come across as hypocritical.
When the writers are trying a little harder, sometimes they'll reference the idea that catching a pokemon limits their powers, especially so for legendary pokemon, which is why they "have" to control them with some flavor of torture machine instead. I'm pretty sure Cyrus states outright that Dialga and Palkia would be useless for remaking reality in a Pokeball which is why he tried using the red chain thing instead.
