I believe that you can't really put them against each other.
If you say "Oh 3D is better because it is cleaner then 2D" or "2D is better because it requires more skill" it just doesn't work that way.
3D you have modeling and other things, while in 2D you do not. In 2D you have to make a way to make the animation not look flat, other wise it will come out funky and lame.
So in reality, when doing 2D you are trying your best to get a 3D effect, not just paper. While sometimes you may be going for a flat environment, most of the time you are not.
In my opinion though, i like watching a 2D animation more then one made in Maya or Milkshape 3D.