In omega ruby and alpha sapphire what is the best Pokemon to use a masterball on?
If you are shiny hunting in the mirage spot use it on a shiny that would usually be hard to catch.
Or you could use it on Shiny Rayquaza
Deoxys
It is difficult to catch, with a low catch rate, and with Mega Rayquaza, quite easy to faint by mistake. Making it one of the hardest Pokemon in the game.
However, according to this reddit post, you can rebattle it, at level 80 by following the following steps:
When you go back to the Mossdeep City Space Center, the scientist on the second floor says Deoxys is near route 131, Unfortunately, it is not on route 131 nor the top of the Sky Pillar unless: Clear the Pokemon League for the second time (First time was your main game), you will now be able to choose your Unova Starter from Professor Birch. (Similar to how you choose your Johto Starter) Now go back to the top of the Sky Pillar. The Deoxys triangular stone will appear there.
When you go back to the Mossdeep City Space Center, the scientist on the second floor says Deoxys is near route 131, Unfortunately, it is not on route 131 nor the top of the Sky Pillar unless:
I have to agree with Empty Boxes on this. I would like to bring two things up though. The cover legendary has a catch rate of 45. Yep. The same catch rate as Eevee and Aipom. And Rayquaza will guaranteed get in any ball without resisting, if I'm correct. So that leaves Deoxys. Or you might wanna use the Master Ball on a Shiny Pokémon.