Trainers take the use of Poké Balls for granted. In the games, they're cheap to the point of ubiquity and make catching 'em all possible. In the anime, they're everywhere, too, holding every trianer's Pocket Monster, except for a certain yellow rodent who stages a one-Pokémon protest. This is seen as one of Pikachu's endearing qualities, but it's possible that Pikachu realizes something that Ash, his friends, and, in fact, everyone in the Pokémon world has overlooked: the “capturing” system is almost certainly unethical.
First, we should establish a pair of fundamental assumptions about how Poké Balls capture Pokémon. We can reasonably assume that the “shrinking” process by which Pokémon fit into their Poké Balls is painless. If it caused injury or discomfort, it's unlikely that any Pokémon would ever obey their trainers. We can also assume the shrinking process keeps the Pokémon within the Poké Ball and does not transfer them somewhere else. The energy required to transfer a Pokémon instantaneously from a storage space to the Poké Ball would be even less feasible than shrinking it into a Poké Ball.
The fact that it took a pair of rebellious, outside-the-box thinkers to expose the barbarity of the system is evidence that the Pokémon world is caught in a plutocratic stranglehold. One of the only major companies in the Pokémon world is Silph Co., the manufacturer of Poké Balls. And Poké Balls alone must account for a substantial portion of a trainer's yearly spending. If an anti-Poké Ball movement took root, it could undermine the Pokémon world's entire economy and bankrupt Silph Co. One of the major drivers of consumption would disappear.
Because of a reliance on the Poké Ball economy, Silph must work hard to ensure that trainers want to use Poké Balls, and they do an excellent job. The reward players receive upon freeing Silph from Team Rocket is not money, a vacation, or a nice watch—it is the perfect Poké Ball, the Master Ball. That sends a clear message to trainers: “help us out, and we will help you—by ensuring that you can capture even the most difficult-to-obtain Pokémon. Without our technology, you know you couldn't capture that Ho-oh.