Firstly I hope they don't try to force in a bad story (at least stop dumping boring, unnecessary dialouge, and let us learn about the characters ourselves), and instead focus on building a cool world to discover. Pokemon (in my eyes) should focus on its core of being a game about exploring and catching cool monsters, which is something that the games have strayed progressively further away from over time. hope gyms return, Sun and Moon didn't really feel like Pokemon games to me with the absence of a series staple. A seamless world (surfing between islands) would make the game feel alot more "whole" and not like a world based platformer a la Mario.
Other smaller complaints include:
Getting rid of the stupid ride gear, I want to role play as a Pokemon trainer, not as a 8 year old with an overprotective mother. Along with more Pokemon to ride, not one in each category.
Make the map simpler, in my experience, games with a simple/clean map tend to feel grander in scale, as it is up to the player to discover what lies ahead, using a map as a simple guide.
Cool it on the 3D level design, the hardware limitations of the 3DS force the world to be small, but the scale of the player model to the environment make it seem much smaller than it should be, and the routes were also much too complicated, only adding to is scale issue.