I wonder what happened if the (3)DS card's too dusty or if the card slot has foreign objects like dusts in it?
If you only you've got access to Wi-Fi then you can breed some Pokémon from your Kalos game. The diversity issue isn't only obvious from the NPCs and important people's team, if you've played the Hoenn games a lot, originals or remakes, you'll notice your team members are similar to your other Hoenn teams. x'D