Out of curiosity, how do you handle the moral ramifications of Pokemon being fully sapient while also still working with the main games verse where Pokemon are kept in Pokeballs? I often run into a bit of a dilemma on how to handle the topic myself, as I very much enjoy writing Pokemon as fully sapient characters in the same verse as humans, but I'm never quite sure how to handle the "they're kept in Pokeballs" topic, other than to do a general hand wave of "if Pokemon don't want to be in Pokeballs, they can break out and just leave", because I'm admittedly concerned that leans too close to a "well they Choose to be enslaved so it's fine uwu" harry potter-esque excuse.
My solution to that is: it's unusual and unsustainable to keep pokemon in pokeballs all the time like we do on the journey
Whatever the original purpose of pokeballs are, in modern time the only thing stopping your pokemon from being kidnapped by other people is by having them connected to your pokeballs yourself. The tech unfortunately exists, it has its benefits, so it sticks around and people just have to deal with it.
Generally, it's treated more like them hitching a ride on you when they don't feel like travelling and wants a little nap (human habitat is fragile and crowded, battling is tiring, and sometimes they're just not built to travel besides you on the terrain you're both at). Much like being in someone else's car, both the trainer and the pokemon expects the trainer to let them out when they get where they're going.
Kids on journey keep their team in pokeballs so often because the journey is an extremely demanding balance between their stamina, the necessary training, and the clock as a League season is only so long. You have to save your team's strength for battling. Even with best practice, Pokecenters still see a spike of traffic after each season as these Pokemon need to recover.
(Is this a lot to ask of an 11yo? Yeah. You're not supposed to win the League on your first try. Even Lance, a prodigy himself, only became Champion at 14. The Kantrio are absolute powerhouses)
You can also mod the pokeball to allow Pokemon to leave the ball by themself. However this disables "nap mode" and they have to stay alert and fully aware the whole trip. This is common practice for service Pokemon