I guess it could be fun, seeing as 3D is easier to work with. The limitatons of 2D mean that they really weren't going to make a crazy huge spriteset's worth of unique animations per Pokemon, but in 3D, they could give them some sort of mind of their own.
Here's an example: Say you aren't moving anywhere for a while. The game can now have idle animations.
The animations are based on three criteria: The nature of the Pokemon, the time of day/how much it's been worked, and how much it likes you.
However, to keep things interesting, no dreadfully uninspired and boring animations allowed. Period (like just because the Pokemon's a Caterpie doesn't mean that all it does is blink, if that (or go into a default battle pose). Don't give all the animations to Pikachu simply because it's Pikachu). At the plainest, a Pokemon can look back and forth to get its bearings, but that's it. I feel like if a Pokemon really doesn't like you, after a few seconds, it should get "angry eyes" and then turn its back on you until you start moving again. If a Pokemon has a jovial disposition, maybe it does some backflips in place. If a Pokemon is a trickster or ghost type, maybe it makes a scary face behind your back. Or steals something from your bag (a prop, not a real item) like an apple and eats it. If a Pokemon really likes you, it'll run circles around you if it's small like Eevee or Rattata (and your trainer'll react and have an n_n face or something). If it's bigger, maybe it'll tackle hug you or something.
If it's tired from it being late at night, worked for a long period of time, or is just a lethargic Pokemon like Slakoth, it'll just yawn and go to sleep. For something Poke specific, Skitty could chase its tail, Meowth could count the coins it stashed to itself, etc.
I think just including stuff like this will give your Pokemon more of a sense of being, because as it stands now, they're just weapons with faces. Honestly, that's all I really want to see in these games. Give me some kind of signs of life with these creatures. I just don't understand why I'm playing a game called Pokemon instead of Advance Wars if Game Freak isn't going to make the effort to have me empathize with the creatures.