I do believe there is a reason. Look at it their way. Suppose that you could obtain Master Balls in vast quantities. Would there be any purpose to the Legendaries? They aren't hard to find, just powerful. If you were to make them captured with one move, their value in link battling would decrease dramatically since everyone would have so many Legendaries. Now look at it as it is. Now, you can get the first Legendary you meet without fail. If you play long enough, it's guarenteed. That gives you some reward for your effort. The other Legendaries, however, require skill, setting apart those who try hard and those who just happen to have the Master Ball. Besides, if you plan ahead, you can get a Legendary anyways. Don't forget that you can save right before battling most of the Legendaries.