This all started with Gen 2.
In Gen 1 it’s established that Silph Co. created it as an experimental ball, and Team Rocket was after it to catch any number of powerful Pokémon without resistance. Pokeballs, Great Balls, Ultra Balls, they all require proving yourself in battle and establishing a connection, like calling out to the Pokémon. Master Balls bypass that. This was a science meant to be used benevolently, but it was nearly stolen for nefarious purposes. Silph Co.‘a president gives it to the player, knowing that they will not use it for evil. It’s heavily implied that it’s meant to be used on Mewtwo, an extremely powerful artificial Pokémon whose out of control power could harm many, in order to subdue it for the greater good, but in order to cater to every form of gameplay, you can still battle and catch Mewtwo normally with any Pokeball.
But then in Gen 2, Elm just gives it to you after you get all eight badges. No fanfare, no purpose, no consequence, no benefit. Just another ordinary ball, but this one catches anything.
You can’t even blame modern games for this. It all started in Gen 2.
The writers and gameplay designers couldn’t connect the dots, or they did and were not able to act upon it, or chose not to for reasons unknown.
