If Pokemon Z (or X2 and Y2) is going to be like the typical 3rd version for X and Y, should X and Y owners download it from the eShop at a cheaper price? If this were to happen, the game would still be sold in retail or eShop for people who don’t own X and Y. However people that own X/Y should be able to download it at a cheaper price.
Typically, 3rd versions of Pokémon games are very similar to the original two versions. While the story and region (to a lesser degree) is new, nothing much changes. The art style is the same with some minor graphical updates and there isn’t any new generation of Pokémon introduced. ORAS didn’t introduce the 7th generation of Pokemon either, but it did introduce Gen 4-6 Pokemon to Hoenn. It's also a remake of a decade old game on a different system. Pokemon Z is going to be on the same system as X and Y.
And although the story of the 3rd Pokemon version is new, the story progression is very similar to the original two versions. The order of gyms and towns you go through is almost the same.
So should owners of X and Y download Pokemon Z at a cheaper price?