The diet is based on the fact that humans (and their digestive systems) have evolved very little since the time of the caveman, but the foods we eat have evolved rapidly. If you consider food processing and preserving methods, factory farming and even the relatively 'simple' art of cooking, a lot has changed in the human diet since the time of the caveman. This is hard to dispute, and I agree with this point. But the Paleo diet also suggests we stick to our roots and eat lots of meat, wild game, nuts and seeds, and avoid anything that wasn't around during the time of the caveman, namely dairy, potatoes, sugar, grains and beans.
While it's great to avoid refined sugars and consume lots of fish, seeds and nuts, that's about as much as I can say is positive about this dietary approach. I can't agree with the 'lots of meat' part, or cutting out healthy sources of fibre. What about fruits and vegetables? We now know that the less meat we consume, the longer we may live, especially disease-free. There is up-standing scientific evidence backing up the fact that plant-based diets are the absolute healthiest ways to eat, including lots of variety in fruits and vegetables as well as whole grains for fibre, antioxidants, vitamins and minerals.
Restricting important foods and taking in an excess of others (especially meats) is never a good idea, unless you have a good medical reason for doing so! Maybe soybeans and yogurts weren't around back when we were club-wielding cave-people, but the fact that they're here today is only to our benefit.