If the game story line and dialogue are good, 2D will never go away. But sooner or later games should adapt. There may actually be another game besides Ar Tonelico 3 that could end up being 3D, I only know the name of the game and the screenshots related to the game. (It's in development though so there are no guarantees).
If this is given an english translation, they better go out of their way not to leave anything out or the same thing that happened to volume 2 will happen to volume 3. I'm also worried they could decide to do alittle editing either on the characters or the outfits just to be safe.