Possibly. At Japan's Pokémon Game Show, The Pokémon Company announced a new animated show called Pocket Monsters: The Origin, starring the original game's protagonists, Red and Green (Blue to us Western fans).
However, during the presentation, a video reel celebrating the franchise was shown - a reel that ended with a scene of Blaziken and Lucario about to duke it out that, graphically, looks better than any 3D we've ever seen before.
This, noticeably, doesn't seem to be from any Pokémon game we've seen yet. Does that mean that a new 3D title is in the works? The Pokémon Company has not made any official announcement about it yet, but hopefully they'll comment on it soon.