One of the big apparent complaints is Gates focus on infectious rather than chronic diseases. From the article:
The same is true when it comes to the foundation’s work in public health. As McGoey briefly acknowledges, the foundation’s investment of more than $15 billion in this field “has done considerable good.” That seems an understatement. Thanks in part to the Gateses’ strong investment in vaccines for infectious diseases, deaths from measles in Africa have dropped by 90 percent since 2000. Over the last quarter century, tuberculosis mortality worldwide has fallen by 45 percent, while over the last dozen years the number of new malaria cases has dropped by 30 percent. And polio, which in 1988 was endemic in 125 countries, is today endemic in only two. The foundation has also played an important part in fighting the spread of HIV and helping those infected with the virus to lead productive lives. For this, Bill and Melinda Gates deserve much credit.
So far so good.
The question is, has this been the best use of their money? As McGoey notes, chronic diseases, as opposed to communicable ones, exact a staggering toll worldwide, yet the foundation has invested less than 4 percent of its funding in research on them, and the global health community has largely followed suit. “The failure to combat obesity, cancer and heart disease epidemics in poor nations,” she observes, “has been one of the most glaring mistakes of global development efforts in recent years.” An equally serious shortcoming has been the neglect of primary-care facilities in the developing world. The initial problems that the nations of West Africa faced in combating the Ebola outbreak stemmed in part from the weaknesses in their overall health systems. Interestingly, in late September, the Gates Foundation, together with WHO and the World Bank, announced a joint partnership aimed at improving access to primary care in poor and middle-income countries — a dramatic (if tacit) acknowledgement that the emphasis on fighting individual diseases has been too narrow.
The primary reason it makes sense to focus on infectious diseases is that once they are gone, they are completely gone. Obesity and other problems don't go away permanently. In contrast if we wipe out malaria or polio, we won't have to deal with it again.
Note also that every single one of the other major criticisms acknowledges that it is something that the Gates have changed already. For example, the article discusses how a number of the Foundation's early attempts at education reform didn't work well. But they changed what they were doing. So they are already using effective evaluations and metrics to decide things.
I find it deeply unfortunate that someone spent an entire book criticizing the Gates Foundation when there are far more clear cut wastes of money out there. The Make a Wish Foundation is an example. They spent 58 million dollars last year http://www.charitynavigator.org/index.cfm?bay=search.programs&orgid=4038#.VljSXnsyH3U and millions more came from businesses in parts of wishes to help a tiny number of dying children, whereas if that money was spent effectively on cancer research, there would be fewer children dying. Instead we have an entire book focusing on one of the most effective and efficient charities in on the planet which complains that they aren't efficient enough.