I think it's a cool concept, but I understand the frustration of trying to reset for good legendarys. I don't play ubers, so I usually don't use legends. Even for OU legends, I just use a master ball and get a good nature, so it slipped my mind how messed up it would make IV hunting.
Still, from a story and in-game concept, I thing it would be pretty cool.
i could totally seeing this happen with previous gen legendaries. let's fight ho-oh and lugia in a sky doubles battle and only catch one. how about a triple battle with one of the trios to really screw things up?