So currently there are some pokemon that are unable to be caught in certain pokeballs, Scythers and Scizors can only be in either a Safari Zone pokeball or a Regular Pokeball, Shedinja can only be in a regular pokeball, and some pokemon such as Shuckle used to be available to be caught in the wild with whatever pokeball you wish but can no longer as they are no restricted to the Safari Zone.
My suggestion would be an NPC similar to the name rater that will allow us to change the poke
This is the case with 90% of pokemon, however it only allows you to continue over with the same pokeball, if that pokemon is unable to be obtained in a pokeball of a certain kind there is no way to change it, such as with Safari only pokemon which if bred will always be in a Safari pokeball, I gave examples of this.
Scyther can either be obtained in the Safari zone in Kanto or via the Game Corner as a prize (which puts it in a pokeball) Nothing can change this via breeding, it just m