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Well, they really have to give (Mega) Zygarde a good role in the ultimate weapon shenanigans that happened 3,000 years ago.
They also have to pace the Team Flare plot better. It seemed to escalate way too fast. I'm not sure how they could fix that though. Maybe by integrating the Emma/Looker subplot into the main game?
Oh yeah, and improve all the rivals. Make Rival Calem/Serena a jerk with a heart of gold or something. Now that ORAS is out, Calem/Serena might as well be known as the most bland rival in the franchise. Make him/her and Shauna, Tierno, and Trevor EARN their right to walk next to you in your victory parade by giving them better teams.
I wouldn't mind more interaction with the gym leaders as well. This is something the Unova games excelled at (Gen IV did this very well too), but the Kalos games regressed in this department.
Character customization should move a bit away from conventional fashion and allow the player to change their hair color to something unnatural like green and purple. It would be cool if there were "costumes" so that you can dress up like iconic characters like Red, Cynthia, or a Team Rocket grunt.
