Where do Xerneas, Yveltal and Zygarde came from and what kind of relationship do they have to the Kalos people? Where did Xerneas and Yveltal live before Team Flare caught them? Where are Diancie, Hoopa and Volcanion living in Kalos? Was the sun clock made of crystal made by Diancie? Does Volcanion have a connection to the power plant?
Where does the Mewtu came from, I mean who created or cloned him? How did AZ invent his powerfull machine?
I think the Pokemon games since Gen 6 won´t explain the background of the legendaries anymore. It feels strange. In Kalos they have Pokemon who can bring live and death and nobody worshipps them or knows where they live.