Coming from the Warmachine side, where we use practically nothing but 2D terrain... It wins on clean play, cost, and convenience. It fails pretty hard on looks, though, and I've had more than a few games where a piece of terrain was misplayed because it was 2D - e.g., someone (me) planned out their turn forgetting that a LOS- and movement-blocking house was blocking their assassination run...
The best compromise, IMO, is to have 3D terrain with 2D templates underneath, so that when models move into the terrain or you need to make careful measurements, you can remove the 3D piece and still have the area template to play with.