I'm completely willing to concede that Mark's daily Apple may be better than other paleo sites because I haven't read enough to know one way or the other.
Is Paleo evidence based? Sure if you ignore the information that doesn't agree with their theories. It's called cherry picking when you do it on purpose or confirmation bias when you do it on accident. Either way, you use the evidence that supports your view point and ignore evidence that refutes it wouldn't be what I would call "evidence based".
I remember reading an article on his cite that excess carbs are turned into fat in humans. This is not true. I remember reading an article making health claims about Primal (Paleo) eating. Well - all of those same health benefits come when you lose weight regardless of diet. It's just over stating what we do and don't know that turned me off. Again, nothing against Paleo eating I often reccomend people try it because you simply can't help but lose weight folowing strict Paelo.
Also, I get it. Telling people half facts about amazing health benefits helps with compliance. Sure enough, someone who is overweight and following the SAD and starts eating Paleo is going to become healthier. They could follow literally ANY diet other than the SAD and they would become healthier. That is why just about every diet book spends the first couple chapters talking about why their diet is special and life changing. If you believe a particular diet is special and life changing you're more likely to stick with it.
This leads me to my last issue with Mark's Daily apple - it's the dogma of "This is the way". It's not THE way it's one way of eating. Ever hear of CRONies?
They think they have he optimal diet. Of course, originally based on rodent studies. There are ongoing studies with monkeys that were looking quite promising but overall it looks like while the CHON diet might be good at warding off disease it isn't extending life as hoped (at least not in monkeys)
I personally intermittently fast. People make all kinds of claims about the health benefits of intermittent fasting and there is some early evidence that it may be true in the way that it mimics calorie restriction. Still, the primary reason I intermittent fast is it makes restricting calories easier and until there is more evidence I always will correct people who taut the health benefits of intermittent fasting.
By the way, on your point of low fat dieting, the studies showing that carbs don't turn into fat is one reason the low fat craze began in the first place. Carbs aren't turned into fat, fat is stored. Thus, low fat craze came into existance. However, people never actually ate low fat and we all got fatter.
If you're still reading this, my suggestion is to read from guys who are truly evidenced based and recognize the importance of context. Lyle McDonald, Alan Aragon, James Kreiger and others are out there but most have never heard of them because evidence and context based advice doesn't make for good headlines which means fewer books and magazines sold. Good headlines are good for web hits but only adds to the average person's confusion.
Finally, wheat. Yes, we can't just eat wheat it must be treated first. Yes, the food pyramid is terrible and used to be worse. This doesn't mean that wheat is bad for everyone. Some people are gluten intollerant. Fewer people have celiac disease but gluten is the new fructose. I think sugar is next. It's just a merry go round of half truths that keep people buying books, magazinea and driving web traffic.
I really love your enthusiasm. I just urge you to check out the guys I mentioned. In particular Alan Aragon for $10 offers so much information through his research review series it is rediculous and Lyle McDonald has hundreds of free articles on his web site.