While the anime has various factors detailing the history of the Poké Ball, the game series has yet to go deep into the history of it. So far, all we know is that the original Poké Balls were made with apricorns.
Considering the huge moral division regarding Poké Balls and trainer battling, both in the games and in real life, it would help to understand just why both of these exist, and why pokemon seem unaffected by it. I would like to present my theory on the subject, and open it to discussion for everyone.
I. THE POKÉ BALL
There have been questions raised about if the Poké Ball is immoral, by both real and fictional people. In Pokémon Black & White, character N labels Poké Balls as tools for coercion. In the YouTube web series The Dex, hosts Alex and PokéKellz acknowledged the possibility of Poké Balls being immoral. Well, why do people have them? Why are characters in the games so dependent upon them?
The phrase, "It's dangerous to go out alone without a Pokémon!" is a commonly heard phrase throughout the course of the series. A common reason stated for why it's dangerous is the fact that wild pokemon jump out of the grass. This poses the possibility that the Poké Ball was created to protect people from wild pokemon. In the game, a wild pokemon can jump out at any given time, and in most cases, they will attack incessantly. As perpetuated, the average human can be badly hurt by any pokemon. However, by capturing the attacking pokemon, a human would be able to survive an attack. This places the Poké Ball into a position of high priority, simply for the sake of people keeping themselves alive. Protection is perhaps the most likely reason for the creation of the Poké Ball. However, why do people who don't travel wild areas still have them?
2. Comfort and Safety
It wouldn't be sensible to not take the pokemon's state into account. It has been mentioned many times throughout the series that people and pokemon have worked together since, like, forever. Prior to the advancement of human civilization, the need for containment surely wasn't as necessary. However, in the modern world, pokemon can't just go running about in cities by the thousands. That, too, can be dangerous. Thus, the Poké Ball is likely utilized in cities and towns for the safety of humans and pokemon alike. In the games, we often only see small pokemon outside of Poké Balls in a city or town. A larger pokemon outside of a Poké Ball is usually helping humans in some sort of endeavor, such as Machoke helping moves boxes and furniture. There may be city (or region) ordinances making it mandatory for pokemon to remain in Poké Balls unless under certain conditions. Much like keeping certain animals caged or leashed in real life, the mandate of Poké Balls ensures the safety of all citizens and their pokemon within a given area.
II. TRAINER BATTLING
As with the Poké Ball, trainer battling has had its moral parameter questioned, most notable in Pokémon Black & White. However, in real life, many have criticized the Pokémon games as being 'supernatural **** fights.' However, in the games trainer battling generally seems to be a mutual and well understood sport, by both humans and pokemon. The question here is, how?
1. Battling is Natural
There have been examples within the games implying that battling is natural for pokemon, possibly a form of comradeship. In Pokémon Emerald's Battle Frontier, the Battle Palace has pokemon battle on their, without any discretion from their trainers. The same is seen in the Verdanturf Battle Tent, also in Pokémon Emerald. In these battles, the pokemon fight freely, using their own judgment to decide orders of attack. Even more so, how they fight depends on the individual pokemon's Nature. This shows that every pokemon, both wild and otherwise, is capable of battling on their own. So, why are there trainer battles?
2. The Virtue of Trust
Perhaps the most common theme within the Pokémon franchise is trust. Parents, gym leaders, and Champions, and professors are stress how important it is for a pokemon to trust their trainer. This is likely because that is the whole point of trainer battling: the sport of battles at the trainer's discretion. Unlike natural battles, where the pokemon are battling freely, in trainer battles the pokemon takes direction from their human trainer. In order for this to succeed, the pokemon must put all of their trust into their trainer, believing he/she can make the right judgment calls. This explains why a pokemon who faints grows unhappy; they regret having trusted their trainer. The utilization of trust and trainer discretion in trainer battling clearly shows the distinction between trainer battling and natural battling, thus removing the possibility of trainer battling being immoral. Or does it?
Not every aspect of trainer battling and the Poké Ball can be covered, and there are still examples that may pose a possibility of either of them bearing an immorality factor. This is where I leave it to you all. Feel free to discuss what may be the most taboo subject for any Pokémon fan.