... nobody understands how decisions are made or how imagination is set free

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John Maddox (1925 - 1999, "lecturer in theoretical physics at the University of Manchester from 1949 to 1956 and editor-in-chief of Nature from 1966 to 1973 and from 1980 to 1995"), certainly not a friend of pseudo-science (see his role in debunking homoeopathy claims) and certainly not a friend of woo-woo (see Wikipedia > The Sheldrake editorial 1981, further elaborated in 1994) wrote this, in a paper published posthumously:

“The catalogue of our ignorance must also include the understanding of the human brain, which is incomplete in one conspicuous way: nobody understands how decisions are made or how imagination is set free. What consciousness consists of (or how it should be defined) is equally a puzzle. Despite the marvellous successes of neuroscience in the past century (not to mention the disputed relevance of artificial intelligence), we seem as far from understanding cognitive process as we were a century ago.” — The Unexpected Science to Come, by Sir John Maddox, (Dec 20, 1999, Scientific American, Vol. 281, No. 6, pp. 62-67)

Was it a fair account of the situation in 1999? Has anything significantly changed since?

The problem has very much to do with methodological naturalism (=physicalism), however loosely expressed. 

Scientists should keep using the method of Natural Science to confront questions about the mind and its relation to the body/brain, even if they should suspect that Natural Science may never give fully satisfactory answers, for the simple reason that the method of Natural Science includes essentially (methodological) naturalism. Beyond, there is philosophical speculation, which is perfectly legitimate, BUT which is NOT constrained by (methodological) naturalism. Certainly fancy divagations like "non-reductive physicalism", or "holism" or some other fancy "-ism" are of no help whatsoever.

Dickerson's "Rule No. 1" ....

Rule No. 1: Let us see how far and to what extent we can explain the behaviour of the physical and material universe in terms of purely physical and material causes, without invoking the supernatural.

... in my opinion is the best definition/prescription of methodological naturalism, explicitly refers to the supernatural (which he opposes to "purely physical and material causes"), which means that any hypothesis about the mind, however limited, that cannot be reduced to physical states is simply non-scientific.