>Speculation
They've lied to us this entire time about the size of the Kalos Region.
Only Pokemon X has actually been shown, as the Coastal and Central Kalos Region, with its open fields and forests. Pokemon Y, however, takes place in southern France, as part of the Mountain Region, containing Massif Central, and a whole different selection of gyms to face.
When you beat the elite four, you get to explore the other region in a National Pokedex and encounter Pokemon not seen in the other version, with a ramped up versions of the older ones. Yes, you can still gain Pokemon from the other games, but they're absent in your game until after your Elite Four is complete. After beating the Elite Four there, you can challenge the gyms in the other region, then face THEIR elite Four, and the true Champion.
