Pokemon Multiverse Theory

In Pokemon Omega Ruby and Alpha Sapphire, during the Delta Episode, Zinnia mentions a world, not unlike the one you're playing in, that would be endangered if the meteorite was warped. She described it as a Hoenn Region, just like the one ORAS takes place in, but the war in Kalos never took place and Mega Evolution was never discovered. That sounds familiar, doesn't it? Just like the world of the original Ruby and Sapphire. Later, at the Battle Resort, Maxie (in AS) or Archie (in OR) says something along the lines of "Maybe in a parallel world, I would've tried to wake Groudon/Kyogre!" - Just as they did in the other version. This suggests that each version of the games takes place in a different universe, each with small differences making them unique. Further supporting this last point is the fact that the device used to warp space in ORAS, sending an object to a faraway place, is called a Link Cable. You know what else is called a link cable? The object that allows two gameboys to communicate. This also suggests that each individual cartridge takes place in its own universe! When you're trading or battling with a friend, you're actually communicating across universes. Cool, huh? MatPat puts this much more eloquently than I do, so you should go watch his video at the top of the page for a more in-depth explanation.