A game that actually takes place during Pokemon X and Y.
OK, so. In Pokemon X and Y, right about when you're about to enter some town, you bump into some random guy. You shrug him off as being unimportant.
Then, in the next game, you're rushing away from the villain when you bump into the PC from the previous game, in the same spot as the last game, thus connecting the 2 universes.
There may be a few other parallels too, such as some of the trainers in Pokemon X and Y may be at the Pokemon Center healing their Pokemon from their battle with the character from X/Y. It probably wouldn't reference any events that are version exclusive, such as Yveltal or a version exclusive gym leader (ala Iris and Drayden).
Now that I've written this, it probably won't happen. Hey, it doesn't hurt to dream, right?
Whenever you think of some new great Pokemon idea, the universe is altered so Pokemon won't use that idea.