I read Thinking: Fast and Slow a few years ago when it was all the hype and was not convinced. I remember many experiments where it was clear to me that the subjects just answered a different question than the one the researcher asked them. And I do not mean that they "anchored" their answers on something else or they replaced the question with a different question because they had no answer to the original question - they just had a completely different understanding of the question itself, and their answers to this question were correct, even in "System 2."

For example, I always had the suspicion (which may be wrong) that in questions like "which is a more likely outcome of 6 coin tosses, HHHHHH or HTHHTT", people tend to understand this question as: "which is a more likely outcome of 6 coin tosses, a sequence of 6 heads, or another sequence without any obvious regularity in it", in which case the latter is clearly the correct answer.

Now, in my experience, people with slight autistic tendencies often have problems with sorting their impressions into broad, general categories, but instead always analyze (even remember) the exact impression (or "special case") they are confronted with. For people like this, the question "HHHHHH or HTHHTT" is a completely different question than for the majority of the population, for which HTHHTT is a class of outcomes, not a specific one.

So, the problem to me does not seem to be a problem with human intuition for probability (or with "System 1", in Kahneman's words), but just one of semantics. If you go further and assume that scientists have a higher percentage of people with autistic tendencies than the general population, then the problem simply becomes one of communication between the researcher and the subject.