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I submitted my first paper to a reputed journal and it came back with major revisions. One review is positive while other suggests to reject the paper. Though the reviewer who rejected the paper was under a wrong impression that a smaller version of the paper had earlier been published somewhere else (I provided a preprint on arXiv and declared so in the cover letter).

I have made significant changes to some sections of my paper and now writing the review text. So my questions are:

  1. What is the etiquette for replying to the reviewers. "Thanks for such comments" etc after each comment seem very repetitive to me and seems they sound just as formality. Are there any established etiquette to reply to reviewer comment (specifically for very negative comments)

  2. Is it OK for the review text to have 5-8 lines in response to comments which are not there verbatim in the revised manuscript. (Since I want to connect to the revision as compared to the previous version)

  3. Should I include the changes (such as tables for new results etc.) in the review text or rather point to relevant sections in the manuscript ?

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    One specific point not mentioned in answers so far is "the reviewer who rejected the paper was under a wrong impression that a smaller version of the paper had earlier been published". When a reviewer makes a factual error, it's important to tactfully but unambiguously correct it. You can simply quote the reviewer's comment and say "The reviewer is mistaken; this paper has not been previously published". If the reviewer is flat-out wrong about something, the editor can put less weight on rest of their negative comments.
    – iayork
    Sep 9, 2015 at 13:00

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The more you write the more people need to read before they get to the stuff they need to know, so I would keep the formalities short. I typically start my response letter with a general thanks to all reviewers. If one has been especially useful I will mention that there.

If there was a comment that happend in all (or many) of the reviews I will discuss that at the begining as well.

After that the letter becomes very "tabular", For each reviewer I just discuss point for point how I dealt with that comment. Usually it is just a sentence and the page (and line) of where that change happened in the text. Occationally it may make sense to write a bit more, and I do so whenever required.

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Different people follow a different 'style' when replying to reviewers. I have seen several different ones while reviewing papers and also while writing my own replies. Based on these, I can say the following:

  1. I generally thank the reviewers and editor for taking time to go through my paper - it is voluntary work so the least they deserve is this! I do not thank them after every comment but if I am making specific changes based on their recommendations I make sure I make them aware of that. For example, "this figure has been changed following your suggestion" or something like that. Because the reviewer may not remember that was their suggestion in the first place (rare, but it does happen). This works specifically for negative comments as you don't have to thank them but if you are changing something partially based on a negative comment then they are somewhat being "acknowledged". Do reviewers care about these? I don't think so but its just good practice. If you are vehemently defending something and not making any change (i.e. sticking to your guns) then you can still explain that politely.

  2. Yes, nothing wrong in that. You can even have a page of comment if you need to especially in major revisions.

  3. That depends on you. I generally don't include it in review text and just point out the figure/table number.

Good luck with your revision and you may find this post of mine interesting about how to tackle a major revision.

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There are many ways to write a response to reviewers, but this is generally how I approach it:

An introductory paragraph, mainly directed at the editor, discussing the broad-strokes themes of the changes. "Reflecting the comments by the reviewers, we have included additional information on the simulation approach used, as well as expanded the discussion of the work's implications in practice. We believe you will find the enclosed manuscript to be significantly improved..."

A point by point addressing of the reviewer comments, formatted something like this:

Reviewer 1:

I think this paper is excellent, timely, methodologically interesting, innovative, and in every way an exemplar of it's kind.

Thank you.

Figure 2. When printed in black and white, it's impossible to distinguish the results of Scenario 1 vs. Scenario 2

We have altered the lines in Figure 2 to have different symbols as well as different colors to distinguish between Scenario 1 vs. Scenario 2, which should improve readability when printed.

Reviewer 2:

I don't trust the results of this paper. The authors used X, when they should have used Y. This is a curious decision that cases doubt on the rest of their analysis

We considered using Y when approaching this analysis, however because of A, B, and C properties of the data, Y would be inappropriate, and yield a biased result. The method we used for X is detailed in Science, P. Methods for using X in Circumstances Exactly Like This. 2013. Society Journal (7)11.

And so on, and so on...

When addressing reviewer comments where your response is "Yeah...no.", I find being firm but polite, and giving a justification, to be your best bet. I don't tend to include the exact changes to things like "This has been reworded to be substantially more clear", but then several major journals in my field require manuscripts with Track Changes enabled to do exactly that.

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