I've heard that legendary Pokemon such as Kyogre/Groudon respawn after you defeat the Elite Four (if you didn't catch them). The only information that I can find seems to relate to the original version of the game.
Can players faint legendary Pokemon in order to progress the story and come back later to capture them? And are there any exceptions?
The reasoning for this is some players, myself included, wish to finish the game in order to unlock post-game features before investing time/effort soft resetting for ideal natures in legendary Pokemon.
Please avoid spoilers where possible.