I had a thought actually, and it's somewhat based on Koopaul's idea. In the games, Pokemon are generally shown as being innocent for the most part, where as humans are generally the problem. What if their was a single pokemon that chose to give up it's heart to become invincible, much like Koopaul said (in the sense that "no heart=no hurt"), but the heart, instead of being a physical heart, took the form of a new pokemon, a more pure version of the original legendary, while the heartless version turned into a much darker, somewhat twisted version. That gives us 2 legendaries right there, one that represents the purity, another that represents corruption (in a sense), and when they come together, instead of combining the two legendaries, it reforms the original one as a new entity (this would be the Rayquaza/Giratina/Kyurem of the group).
Either way, in the versions, it would still stand to reason that you could only hurt one pokemon if you have it's missing side, so it still follows Koopauls idea to a certain degree, it just takes a slightly different approach to it by making it so that not only would the enemy team be to blame, but so would the legendary pokemon itself.
Either way, in the versions, it would still stand to reason that you could only hurt one pokemon if you have it's missing side, so it still follows Koopauls idea to a certain degree, it just takes a slightly different approach to it by making it so that not only would the enemy team be to blame, but so would the legendary pokemon itself.