Wow, the in-game Pokédex... what I'd like to see in Pokémon X and Y with the in-game Pokédex... is the ability to look at the Pokémon's in game model... knowing that it probably would be very likely to happen. I'm thinking the cry effects used in the Pokédex from Black/White would make a return in Pokémon X and Y.
And oh! What about viewing it's habitats to know which locations it can be found? I'd love to see a 3D model of the map in a GPS-syle of things, showing the glowing areas in which indicates where it's found.
But viewing different formes would make a return as well, probably even viewing their 3D model of those formes as well.