>>53774148Legends Arceus and the Mystery Dungeon games do this. But there is a lore justification for using boxes, Pokemon can naturally shrink themselves, its how they hide in tall grass (this was true for the original lore as well as more recent lore from games like PLA) and after you tame them, they actually enjoy shrinking down into their Pokeballs. So teleporting them to presumably some offsite warehouse via the PC actually makes a lot of sense.
Also, if you think that bit of lore is retarded, then you're right, but also remember that its lore thats written for a franchise designed to sell merchandise. Pokemon that couldn't be shrunken down into capsules wouldn't be as marketable.