Oh yes, cinematic animations has been becoming even more common than ever before in the main Pokémon games, especially with Black Version 2 and White Version 2 having several cinematic animations of Team Plasma's Frigate and battling Black/White Kyurem.
It's a very high chance that cinematic animations would indeed occur much more frequently in Pokémon X and Pokémon Y, because of it's improved 3D graphics capability. And now we'll be able to see the trainers in the cinematic animations as well, instead of some basic sprite.
