I used the master ball on Reshiram, planning to keep resetting until I could get a good nature(I didn't realize he had a high catch rate, and wouldn't take long to catch with another ball). But I couldn't check It's nature until after cut scenes and two battles, and after I did that i didn't care, I just didn't wanna do it again. For me the final battles were just a nuisance I was trying to get over and done with so I could check Reshiram's nature, rather than an epic conclusion. Well I guess that speaks volumes about the difficulty of the game.