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I have to go with mewtwo because with his high special attack you only have about 20 turns to catch it which most of the time is not enoguh. And his recover really makes me made but I have caught every legendary pokemon without a master ball except raikou and entei
I'd say the three Guardians of Ho-oh, because of Roar and/or fleeing. Of course the Regis are a pain because of their strength and tenacity but at least they are stationary.