I am trying to figure out which Pokemon to use my master ball with.
There are numerous legends in B/W 2 that have the lowest catch rate, 3.
It's all up to you. I would use the Master Ball on the one I want the most, and that's what I recommend doing.
Source: http://bulbapedia.bulbagarden.net/wiki/List_of_Pokémon_by_catch_rate