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.
So, a Pokémon is captured painlessly and then stored in its Poké Ball while it waits to be released. If a Pokémon is kept in suspended animation within their Poké Ball, they will be confused and disoriented every time they are released for battle. A Pokémon will be summoned for use, and when it completes its task (knocking out another Pokémon), it will feel a ball bump against its side, see a flash of light, and then—nothing. It reappears somewhere new, called upon to fight a different creature, possibly in a place it does not recognize. And the process repeats hundreds of times during a Pokémon's life.
The situation is worse if a Pokémon is fully aware of its surroundings from inside a Poké Ball. Whether or not the enclosure is lighted, there is very little room for a Staraptor to spread its wings, a Stantler to spread its legs, or a Snorlax to spread out and sleep. Keeping a Pokémon able to hear all the sounds of the world outside its Poké Ball but prevented from seeing any of the world around it is incredibly cruel. Before capture, Pokémon roam free; being held in a small box, unable to roam, would be a Pokémon rights travesty worse than any animal zoo in the non-Pokémon world.
The only group in the Pokémon world that has expressed any reservations about the way trainers capture Pokémon is Team Plasma . While Plasma is fundamentally corrupt, its founding principles provide compelling arguments. Keeping Pokémon capture local and avoiding it when necessary seem like eminently reasonable pursuits for trainers. Reducing the reliance of trainers on capture via the Poké Ball and requiring relationships to be built on trust and mutual benefit seems more positive.
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.
The Master Ball never fails.
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.
The standard routine for captured Pokémon is clearly unethical. Leaving Pokémon in Poké Balls for the majority of their day and releasing them at random is confusing and disorienting even the best-case scenario. There may be times when it makes sense to keep Pokémon in Poké Balls, such as while riding a bike or taking a bus or train. Similarly, large Pokémon like Steelix or Wailord may not be the best candidates to take for a stroll on a narrow path. But this should be the exception, not the rule.
Pokémon should be kept out of their Poké Balls whenever possible. The Poké Ball is a cruel, corporatist device that benefits only the moneyed interests in the Pokémon world. Poké Balls trample on the rights of the creatures that make Pokémon trainers successful, and distort the moral compass of trainers who should—and occasionally do—know better.