At the heart of the story is the notion that there is no hard scientific studies showing the Paleo diet to be more effective than the standard diet recommended by most health authorities. This is not to say there aren't many studies that show a Paleo diet to be more healthy than a Mediterranean Diet for several populations, there are several. What it says is that these studies do not have enough participants to make a clear determination as to whether the diet is better than what health authorities currently recommend.
In my opinion, this is a valid point. However, when these same health authorities point to the healthfulness of processed food products such as whole grains, they are using data that cannot be used to make that determination. One of the inherent problems with nutrition research is that you have studies that are well controlled that can be used to say A causes B. Since these studies are well controlled they tend to have a very small number of participants because they restrict external influences that may affect the results. Theses are the types of studies that are coveted by scientists, but they are extremely expensive and hard to do and, therefore, quite rare.
On the other side of the coin are studies that can have a huge number of participants but that aren't controlled at all. No matter how many people you have in these studies, you can never say A causes B because you aren't testing whether A causes B, you are testing whether there is a relationship between the two. This second type of study is where most, if not all, nutritional recommendations come from. The problem is, using these studies to say eating X improves health is essentially lying because the studies do not say A causes B or B causes A, they say A and B share a relationship that deserves further testing in a well controlled experiment.
In the very few well controlled experiments that experts use to show whole grains to be healthy, whole grains are compared to refined grains as a control group. In effect, these studies do not show whole grains to be a healthy part of a diet, it shows them to be healthier than refined grains, which we know to be fairly unhealthy. Of course, it's difficult to identify which type of study the health authorities are using to refute the Paleo diet in these articles since they don't post any references.
On the logical fallacy end of things is the point that our ancestors ate seeds of grasses, which is a fair point. However, comparing a loaf of Pepperidge Farms bread to the types of grains eaten by our ancestors is hardly a scientific comparison. For one, the traditional way to prepare grains is to soak them, which aids in digestion and cuts back on some of the toxic properties of grains. Secondly, grinding grains with a mortar and pestle is hardly the same as the modern processing of grains in to bread by machine.
Another logical fallacy in these arguments is that grains are somehow necessary to a healthy diet. While this is not directly stated in these articles, it is implied by the notion that cutting out grains or specific food groups is detrimental to health. While the authors like to point out that the diet of our ancestors varied greatly, and many included seeds of grasses(grains), this notion does not in anyway imply that grains are necessary to health. In fact, many modern hunter gatherer societies don't eat grains and do quite well.
While I agree with many points health authorities make against a Paleo Diet, particularly that a high meat/low carb/low diversity diet is a good idea, I feel these arguments are against the lunatic fringe of those implementing the diet. A lot of this has to do with earlier iterations of the diet and the now increased availability of the books and sources that promoted it. Over time, the message that Paleo diet proponents have crafted has become more refined and more scientifically sound. A great reference for what I believe to be the future of the movement can be found here. Rather than pointing the finger at macronutrients such as carbs or fat, the modern processing of food and it's effect on the microbiota of humans is implicated.
While I don't think this will quell the influx of experts who argue against the diet, it will certainly make it more scientifically valid. None of this is to say that a rigid Paleo diet is absolutely necessary for health. However, making better food choices a majority of the time based on principles identified by the science being generated from principles of evolutionary health can only be beneficial in the absence of hard scientific data that shows one way or another that processed grains, whether whole or refined, are something healthful to eat. That data, despite the insistence by health authorities, does not exist.