I love the idea of the cathing legendary pokemons but I think the system can use some polishing. I'm talking about the fact that you can't try to catch a second version of X legendary pokemon.
What if, like when you kill X legendary pokemon you can go to the trainer valley and beat a trainer (forgot his name) to get another shot at battling, and then catch the legendary pokemon, you could try to recatch a legendary pokemon that has really bad iv's, or the wrong nature. You would have to release the original pokemon though, also you should only be able to do this once a month.
I think this would be better than the system that we have now. On the handheld games you could just Soft Reset for the right IV's and nature. In PRO this is not possible and the only way to get another shot at catching is starting all the way over which takes ages if you're already far into the game.