Only Gamefreak would know...
Within the same generation, you'll likely have two different regions. Those regions have differences in between them to have a clear distinction between the games. Or else it would be somewhat boring, playing through the entirety of ORAS seeing the same X&Y sprites you've encountered over, and over again.
With regards to the remakes games, such as ORAS, HG/SS, and FR/LG, the remakes attempt to somewhat mimic the style of the game they are remaking (RSE, GSC, RBY). However, they need to keep the sprites modern to go along with the games within the same generation. Therefore, it is logical for them to use different sprites.