Tapu. Freaking. Lele. Not because it's hard to catch, but because it refuses to have the IVs for HP Fire.
Everything which directly runs away from you. Entei was so cancerous. I gave up and caught it with a Master Ball.
People remember this is in the Safari Zone, is not about pokémon in the games, is in the catcher. Regice, that thing ate at least 150 balls before I finally got it.
Any Pokémon? Mewtwo. Takes forever to find, and when you do find it, you only have 2 balls. If it must have been caught: REGIROCK.
Registeel or Raikou...I think Raikou might have the edge over it. Although that's probably because I found a shiny one in the boost before the one we just had and I lost it and god damnit I am still sore over it. Registeel just...consumed balls, though. Like, 50 of them. Such pain.