Ugh, where do I start.
1. More advanced character customization
Yeah, the outfits in Pokemon X and Y were fun to wear, let a small amount of selections for males. Females had more choices for hair and much more clothing, so I would like to see more clothing options that are equal for each gender
2. More things about characters
This would be great. Favorite color, age and birthday for your trainer! Make it more you!
3. Go to each region
This might be frustrated for the people who work on the game. I would like for the trainer to go to all 6 regions (maybe even 7 since Sun and Moon might be a new region)
4. More gender selections possibly?
Our generation now has transgender people and other people. Pokemon should allow more genders for people who might be offended by just "boy and girl option"
5. Finally, Pokemon following you around
Just like in Pokemon Yellow, HeartGold and SoulSilver, I would like the 3D Pokemon following you around as you travel.