The two highest-rated legendary Pokémon in Scarlet and Violet are the cover legendaries, Koraidon and Miraidon. These two Pokémons are the hardest to capture and require you to use your Master Ball on one of them. You should only consider using your Master Ball on either Koraidon or Miraidon.

Should I use a Master Ball on Miraidon?

Additionally, the extra Koraidon or Miraidon players get, depending on their version, is also a solid choice to use the Master Ball on. Regardless of who players choose to use it on, it's better to use it than just letting it sit in your inventory unused.

Who should I use Master Ball on Brilliant Diamond?

It's recommended for players to use the Master Ball on the rarest Pokémon that wander around the region. These creatures will flee after one turn, making them difficult and annoying to catch.