Some tips on what to do and not to do when revising papers and writing rebuttals (I keep repeating this to every new person joining my team so here it is):
Most reviewers want to feel they’ve made a positive contribution to the paper, hence they want to see what you changed in the paper in response to their comments. They want to see very little of responses/apologies/arguments for how they’re wrong. Even when reviewers are wrong, they’re not really, they’re simply mislead by our lack of clarity. Hence my advice is to always put your energy on the changes to the manuscript while making responses as short as possible – the changes to the manuscript should be so clear they are the actual response, which at the same time pre-empts similar concerns by our readers. Remember only about 2-4 reviewers see your responses while our entire community of readers only sees the manuscript (exceptions in journals that publish reviews).
Example below:
Reviewers comment in italic, our responses in normal font, and changes to the manuscript in bold.
Reviewer says: issue A is unclear. Why did the authors chose B over C?
Our response: Apologies for being unclear. We now make this issue clearer by making the following changes to the document:
Issue A was addressed in the following way ….. We opted for doing B because…. C would be an alternative, however….
This bit of the text should be longer than the response. The reviewer doesn’t want to read about why his/her reasoning doesn’t make sense or read a long argument. Instead, the reviewer wants to see that their work made a positive impact on the paper by seeing we’ve made significant changes to the manuscript to take their feedback on board. Hence this bit of text (changes to the manuscript) should be relatively longer than the “our response” bit.
Reviewer says: issue A is unclear. Why did the authors chose B over C?
Our response: Issue A is explained on page 13 (please read paragraph 3). We think B is better than C because…. We could have done C but C doesn’t make sense because… and this response goes on and on for lines and lines of argument that no reviewer wants to read. Plus see the tone is such that we’re basically telling the reviewer he’s got it wrong (dangerous move) or didn’t read our manuscript properly…..
Argument keeps going
Etc
Still arguing why we wont do it
You got the picture.
We go on to say please see text changes on page 12 (but don’t copy and paste there), please see figure 5 (not there), and see our responses to reviewer 3 point 5. I’d advise you don’t do this – reviewers are busy and don’t want to go in between documents or search for their answers in responses to other reviewers. Much better you save them time by copying and pasting all changes including figures in the rebuttal so they only need to see the rebuttal.
Finally we say: But we have made the following changes:
Issue A was addressed such that this and that, full stop.
(this is so disappointing for the reviewer, who's trying their best to improve your paper for free)