I am a tenured professor of engineering at a major research university. Recently, I was asked to review a manuscript for a top-tier multidisciplinary scientific journal. The authors were all grad student or early career faculty, except for one who is a National Academy member (but neither first author nor last author), a well-known person in the field, and a close collaborator with the other authors and the handling editor.
The manuscript was of reasonable quality and worth publishing in a specialized journal. However, it had a couple of serious flaws that, in my opinion, made it unacceptable for a broad, high-impact journal. I legitimately felt as though I could not recommend it for acceptance, knowing that its publication in this journal would give it - and the flawed approach on which it is based - undue credibility.
The paper underwent three rounds of review. The other reviewer accepted after two rounds. I recommended rejection each time. Then the editor accepted the manuscript without even soliciting a third reviewer.
I think it is pretty obvious that the manuscript was accepted based on the reputation of the National Academy member (and their relationship with the editor), and not based on peer review. If peer review actually mattered here, then a third reviewer would have been asked or the paper would have been rejected. The fact that this did not happen makes it seem, to me at least, as though the outcome was decided before the reviewers even saw the manuscript.
So this leads to my questions.
First: Is my complaint legitimate? Is it a fair assessment that this journal seems to be using a "good ole boys" system for evaluation rather than taking reviewer reports seriously?
Second: If so, what should be done? How can I raise this concern with the journal without compromising my anonymity? What protections could I expect against retaliation from the authors, editor, or both?