I have to say I want Pokemon to show up depending on what time of the day it is. I also want another nice plotline to the story that has a lot of meaning to it, like Team Plasma. Team Galatic was nice, but I don't really understand why they did all those stuff in the games.
I also want there to be a female rival for once- Bianca wasn't much for me. She reminds me too much of the DP rival, and the idea annoys me. Like Silver or Gary, I hope for her to be either mean or seriously annoying and make you actually want to battle her. If there's a male, I hope we can at least name him.
If the game were turned into a manga, I also hope that the characters will be named after the games: X and Y. Even though that sounds silly, there's N, who, was named after an alphabet in the animation, the manga, and the games.
There's not much more that I can ask for.