Since the plushes of pokemon in the secret base use the overworld pokemon’s sprite, why not allow the player to put down a figure of their lead pokemon? It means you don’t have to manually add every pokemon to the shop, each base would be more unique to that person’s playthrough, and you could show off all the shinies, deltas, and other rare pokemon you have caught. Most of the bases right now aren’t too interesting or different from each other, so being able to add that personal touch would go a long way, especially for post game bases.
Maybe in a Nuzlocke, you could allow players to put down fainted pokemon that aren’t following you so they can create a hall of fame for their lost pokemon.