I am strongly against 3D in principle, but yes, in this case it is pretty crucial. The remarks Herzog has made about how it had to be in 3D do not, in this case, happen to be bullshit. It's really a meditation on a very otherworldly space, and the bulges and concavities and formations are what give it its character. I would imagine it would be almost flat-out boring in 2D.
The film is sedate by Herzog's standards, not very nutty until the last two minutes (great final shot), but I found it entrancing.
One thing that really impressed me about the crazy motherfuckers who did those paintings--apparently they only went into the cave for the specific purposes of lighting a fire, partying, and painting animals on the wall---and there were bears and shit in there! That's dedication to your art!