Considering how glacial the pace at which Game Freaks develops and substantially changes their Pokemon games, I think the Pokedex 3D is proof that whenever Pokemon 3DS gets announced it'll be a huge step forward graphically. Why else would they not only render all the new pokemon models (high quality -- imo the best on the 3DS!), as well as animate them with attack animations?
Coming from a company that has long milked its franchise, it would baffling to think they'd done all this work for free. I strongly think the next Pokemon game will use assets/animations from Pokedex 3D.
Here's hoping for an announcement soon and that they skip over the inevitable "Grey" version.