All pokemon will have a sidestep animation, for when the player turns around and crosses path with them. Pokémon will interacti with: their trainer, other Pokémon, other trainers, the environment. There will be angry animations, swimming animations, relaxing animations, idle animations, finding something animations, joyful expressions, jumping and so on. Flying Pokémon will have also resting behaviour and aerial maneuvers to perform, as well as swimming ones.
• AI: the Pokémon will not blindly follow the trainer at the same speed: if they find something they may stop and then catch up. More than this if the player stops moving, to talk or simply because he has something to do IRL the Pokémon will start an "Idle behaviour": it will wander around, interact woth surroundings, rest, peck the trainer and so on.
• Fight animations: more moves will come into the game (many of the scrapped ones for LGPE). Many Pokémon will have personal interaction with at least some moves: Typlhosion Eruption or lava plume, Venusaur solar beam, Skarmory steel wing etc.. As well as contact move will involve the Pokémon actually making contact with the proper body part (fists, jaws and so on). More than this there will be a sequenc of animations during battle that wil show Pokémon interacting with their enemy and with their allies (Blissey for example will cheer up the ally in a 2 v 2 battle)
All this graphic work, that is not fully explained here (forests will be different, as well as interaction with items etc..) is why Game Freak has split into two teams and has already started a lot of work for the diferent projects because they will require way more work that ever.