I've recently been trying to get one of my papers published, and have come across the following issue. I started by submitting it to a fairly high-impact journal. It got three reviews, two of which were positive. The third reviewer seemed to find it personally offensive for some reason and hated it. I felt I could respond to all the comments (the negative ones seemed to me to be based on a misunderstanding of the basic premise of the study), but unfortunately the paper was rejected outright without the opportunity to respond.
So, I edited the paper based on the previous reviews (attempting to address all the comments I received, major and minor), re-formatted it and submitted it to a middle-ranking journal in my field (ecology).
This time, the paper received two reviews, both of which were largely positive - mostly minor suggestions for improvement and comments praising the paper. However, the editor said that following comments from an "informal review", he has concerns about the methodology. When describing this he uses the exact wording used by the negative reviewer from my initial submission. Once again, the paper is rejected without opportunity to respond to the reviewers.
I find this very frustrating - both the actual reviews were positive, but the rejection seems to be based on an "informal review" that I'm unable to see, or respond to.
To me, this isn't how the peer review process is supposed to work. Do you think it is worth emailing the editor to appeal his decision? Or is it a waste of time, and I should submit it to another journal?
EDIT: As an update, I emailed the editor and surprisingly they changed their mind, agreeing that I could respond to the comments and re-submit. I did this and the paper was accepted. A good outcome I suppose, though I will probably avoid submitting to the same journal in the future.