I think with the 3DS's StreetPass thing, it can do the whole "secret base" thing from RSE. It would work great imo, since it (theoretically) allows a lot more secret bases to appear in a game (I don't know how the game would handle 2 bases in the same place, how did it handle it in RSE? I don't remember), not to mention how the secret bases would look neat with the 3D and all the cool decorative pieces.
If an RSE remake comes out for the 3DS (since iirc the games cannot be played in a 3DS), it'll probably be saved for that, but I'd like to see it in X and Y.
EDIT: Also, while not directly related to X and Y, the WiiU would make an AMAZING platform for a Stadium-styled game (since the hand held screen makes it more like the DS games, except on the big screen with a machine that can run better graphics)