I'm not attacking Sisson's framework. I haven't read much of his stuff, but the Primal Blueprint does seem to base a lot of its information off of assumptions about what Paleolithic hunter gatherers are supposed to have eaten.
The article above makes a pretty good case for why building your diet from this foundation may not be the most reliable framework. If Sisson is using the latest scientific research to develop his system, then fine. But this is hardly a "Paleolithic" diet then. Why not just say "Avoid processed foods because they have been shown in numerous studies to have negative effects?"
You've implicitly assumed that the strategy is not also informed by contemporary research, but the particular framework being criticized, that of Mark Sisson, makes extensive reference to contemporary research.
In fact, a reader of Mark's Daily Apple is probably linked to more peer-reviewed articles than a reader of, say, Scientific American. Consider e.g.:
http://www.marksdailyapple.com/the-definitive-guide-to-resis...