Disclaimer: I've only read Stone's free eBook. Maybe his evidence is stronger and his ideas better substantiated in his other eBooks (as he claims).
While Stone claims to be basing his ideas on scientific evidence, his dislike for low-carb seems to be based on anecodatal evidence--his own experience of eating moderate carb (100g/day) and anecdotal experiences of friends/acquaintances. As others have said, someone can eat low/mod carb (or paleo) and eat badly. And exercise too much, eat too much/little, sleep too little etc.; it's the whole picture that makes a difference. His experience doesn't mean that LC/paleo won't work for you CarnivorePrincess.
Two of the main differences I picked up bewteen his approach and paleo were 1/ the addition on vegetable starches such as potato, which he is a big fan of and 2/ the phase of weight-loss he advocates where you eat a lot of 'everything'. To deal with these two points individually:
1/ his 'scientific evidence' for this appears to be based on a fairly simplistic analysis of the change in diet of the Pima Indians and its affect on them (from 70% carb to 44% carb--in a different form; from no diabetes and obesity to very high rates of both). His take home message form this is that carbs (starchy vegies in particular) are OK, something else must be the enemy. On the surface this looks likew a reasonable argument, but there are a lot of other factors that could come into play. And who's to say that their previous diet was actually good for them, apart from the stated low diabetes and obesity? So his 'eat starchy vegies' message does not appear well substantiated.
2/ the 'high eveything diet' (HED) that he pushes as a first stage at first glance sounds ridiculous, but on further thought I'm coming around to the idea, at least for some people. Remember he's not advocating eating sugars, fructose, omega 6s, grains etc. it's really on the starchy vegies where his ideas about diet deviate from LC and paleo. So the eat everything actually means eat lots of (what he defines as) good stuff to get past the 'starvation mentality' that our brains can get into when we start to feel that food is scarce (e.g. afetr we go on a low calorie diet). As a cure for starvation brain, this might actually work for some people. I see the goal with eating as to eat 'naturally', including knowing what feels good, the amount that we need, etc. without needing to be preoccupied with eating too much or too little. If the HED gets one to that state of mind and body than that would be a good thing.
Remember that study where they took a bunch of healthy, active young men, put them on a low-calorie diet for a while, and they turned into wrecks? After the diet they became obsessed with food, found it hard to regulate their eating, and just couldn't get back to the state of mind (or body) where they were before: eating to live and enjoying it without being preoccupied. Instead they were living to eat, metabolism was messed up, stress hormones high etc. in short they developed 'starvation brain'. So for those of us who have experieinced starvatin brain, maybe the HED would help--dunno.
As for Stone himself, I support anyone who has a genuinely open mind and keeps learning and refining their ideas. Now that Stone has a vested interest in a particular paradigm (i.e. he has put down recommendations in eBooks, into which he has put time and hopes to make money), he now has a vested interest in that status quo. Most of us will tend to take in new info with blnkiers on once we have reached that stage. Let's see if that happens to Stone.