Here's my opinion on the matter. This goes for Anathema too:
Keep the 2.5D for the backgrounds. Create your tilesets and scenarios with a 3D program, BUT when inserting them into the game, use a color-reduction tool with a fixed palette of vibrant colors to make them blend nicely with the sprites.
I'm fairly certain that this is what Konami did on the DSvanias, because the color count on those backgrounds is CRAZY high to be done purely by pixel-art. Not only that, but I can spot numerous instances of automatic anti-aliasing and numeous others of automatic shading, slightly corrected with traditional pixel-art.
Keep the enemies and characters in pixels only.