I used mine on Rayquaza because I didn't have many other poke balls available, not to mention I forgot to save before Rayquaza's appearance. :pink_blush: Mewtwo would have been a better choice in my opinion though, as I really like it when the color scheme of a pokemon matches the colors of the ball.
//Edit: And I just now notice that this is the XY section and I was talking about my master ball usage in OR. My bad. And there's no Mewtwo there. Double bad.
In X though, it seems I still have my master ball and I've already caught all the legendaries that are available.