I just bought Pokedex 3D Pro, so I really really hope they DO make an update. I don't see why they wouldn't, to be honest. They went through all that trouble to make cleaner, beautiful 3D models of all the Pokemon for SOME reason. Not just so they could dump it all away next generation. Although I'm under the theory that they took 3D Pro's models and cel-shaded/changed them up slightly for X&Y. That picture of Pikachu's model comparisons posted earlier really seems to add credence to this theory. Both models have the same stance.
And I've just actually watched a video of the demo, and made a comparison to a few older models... and I see that they probably ARE the exact same models, just downgraded a bit. The idle and overall look is exactly the same. ...Wow, Nintendo, pretty sneaky.
Due to this, they might not make an update... which kinda upsets me. But I'm still optimistic. I mean, they might just show the shiny cleaner versions of the models and add something to the game anyway as a companion guide to X&Y, 'cause the games don't typically tell you all the moves the Pokemon learn. (I'm really just in it for the absolutely stunning 3D models. @_@ They make it easier to art reference.)