My 2cents on going to 3d as someone who makes stuff in pixel, hand drawn, and 3d.
3D is better in that it's going to allow for more complex, if less stylized, scenes, and possibly more in game variations on animations. Plus, he could potentially open up to having 3D environments to explore in, which I wouldn't mind the game taking on more trappings of something like Silent Hill or Resident Evil, though that's just full speculation on my part.
At the very least, I do like seeing the experimentation, and hope that it goes great.