I’m not quite sure what you’re asking, but basically this all hinges on what is apparently one of my more controversial beliefs – namely that Pokémon choose to be captured. Here’s the short version. We know that you need to weaken a Pokémon to catch it, but also that if you actually knock it out, you can’t catch it – it needs to be conscious (which to me suggests that we’re looking for consent). We see in the anime that there is a tendency to portray battles with wild Pokémon as a process of earning their respect, and this becomes more pronounced as the series progresses. We know that Team Rocket and other villains capture Pokémon both traditionally, using Pokéballs, and with a variety of other contrivances (nets, pits, machines, etc) – the latter is regarded as a heinous crime, even when their targets are wild; the former is apparently totally fine. We know that Pokémon can actually leave their Pokéballs without being ordered. We know that villains use cages to restrain Pokémon, which would be an expensive and illogical waste of space if Pokéballs were capable of doing the same job. Honestly it seems to me like the creators have actually built in a lot of reasons for us to think that Pokémon have a choice in all this.
Also, just putting it out there, Stockholm Syndrome isn’t magic. It doesn’t automatically happen to everyone who experiences a kidnapping or hostage situation. I don’t think you can realistically build an entire civilisation on it, especially when the ‘captives’ are vastly more powerful, physically, than the ‘captors’ and in many cases at least as intelligent.
