I mean, they laid the groundwork 20 years ago if you look around for it. They made a huge emphasis (and still do to some extent) to show how Pokemon are intelligent beings and humanity is in a utopic state where they work alongside nature and pokemon to achieve goals. The anime emphasizes how a pokemon can defy a pokeball even after capture and can ignore a trainer's orders if inclined to. Pokemon have been shown to prefer or not prefer battling and have their own personal aspirations. some supplemental works detail how a pokeball is extremely comfortable and adapts to provide an environment that is suitable for each mon.

It's a razor-thin line but The Pokemon Company put a lot of advertising money into painting that clean image. Which is why it's survived years, decades of narrative against them, even from other million dollar corporations trying to argue animal abuse.