I was thinking of when you enter the Pokémon center to heal your Pokémon to the nurse and you hand over the Pokeballs. The machine shows all of the Pokémon you have on you when it is healing by showing a regular standard pokeball. Instead of it just showing 1-6 Pokémon you have on you showing only a regular ball, why not have each Pokeball reflect which ball you actually used to catch that Pokémon with.
For example, 3 Pokémon were caught at the Safari Zone and 3 others were caught with a Moon Ball. So when you went into the Poke Center to heal with the nurse, you see the 6 Pokeballs you used for each Pokémon by seeing 3 Safari Balls and 3 moon balls on the machine. I know its not a big suggestion, but I thought it would be a little cool to see what Pokeballs were used since technically that's what your Pokémon are sitting in.
For example, 3 Pokémon were caught at the Safari Zone and 3 others were caught with a Moon Ball. So when you went into the Poke Center to heal with the nurse, you see the 6 Pokeballs you used for each Pokémon by seeing 3 Safari Balls and 3 moon balls on the machine. I know its not a big suggestion, but I thought it would be a little cool to see what Pokeballs were used since technically that's what your Pokémon are sitting in.