The fundamental concern with a second layer of review for holders of more than US$1 million in grants from the US National Institutes of Health is that it takes us further from a meritocracy in which the best and highest-impact science is supported (Nature 489, 203; 2012).
Elite grant recipients have gone through reviewers' scrutiny and proved their productivity many times. Reviewers and grant administrators already check for potential funding overlap, one of the issues the reforms are designed to address. Peer review may be imperfect, but it is done by the scientific leaders in the relevant field, and there is no reason to believe that the judgement of an advisory council is superior.
The reluctance of most funding agencies to pay for research infrastructure necessitates either leveraging economies of scale from multiple grants or belonging to an academic institution that is wealthy enough to share the costs — a position not all researchers enjoy. The new policy would mainly affect the most productive principal investigators with multiple R01-type (individual project application) grants, widely considered to yield the most innovative research.
Taxpayers have the right to make the scientific community accountable for improving health, but this extra scrutiny may compromise attainment of that goal.