I caught Xerneas in a Quick Ball because of the X and the color scheme. (I didn't throw it on the first turn to exploit the Quick Ball's function; I wanted to see Xerneas's moves on its unique battle arena before catching it.)
I caught Mewtwo in a Premier Ball because of the color scheme. I generally save my Master Ball for shinies I have a chance of not catching or other rare situations. Also because using the Master Ball on a legendary instead of engaging it in MANLY COMBAT is 2boring4me.
Obviously I'm going to be trading for Yveltal, but were I to catch it I'd probably use a Dusk Ball. Nothing really has a Y motif or comes terribly close to its color scheme, but the Dusk Ball and its associated opening/closing effect seem appropriately loledgy.
