Most of the reasons why Game Freak didn't show the Pokémon using Fly or Surf... is due to the graphical limitations of the hardware, and even the Nintendo DS itself didn't have enough in the way of space to do this kind of thing.
We probably will see a change in this at long last, it would be great to see your own Pokémon actually using the move, such as the player getting onto the Pokémon rather than the character getting onto some shadowy figure. It would be really nice to actually also see the player get onto the Pokémon while flying into the air, it would be amazing... showing the detail of the animation.
I do believe it would improve in Pokémon X and Pokémon Y, and I really hope it does!