Academic writing, whether it be papers, books, dissertations, reports, or even proposals, need to prove that research and data is relevant, reliable, and representative. The body is where an academic does this. So if there are questions about your research, you need to determine if 1) you have described your data, analysis, and methodology in a way that the reader/reviewer understands (easily rectified if you haven't) or 2)the reviewer/reader has problems with your data, analysis, methodology, or underlining theories (harder to rectify).
In the first case, one recommendation I had in revising my dissertation was to write as if I were giving the reader instructions on how to replicate my work if they wanted to do the research themselves. Often we assume readers understand the methodology we use when in fact they may not. I have often had to look up the methodology as outlined by a specific author when reviewing articles or reports. If you don't provide citations or definitions/assumptions that have informed your research, you leave interpretation of your methodology to your reader. A good example is "grounded theory". There are many interpretations of how grounded theory can be applied. As a reader, I'd want to know what process you used and what was the basis.
In the second case, you may need to analyze where a reader might be having a problem and decide if you are going to make changes. If you decide not to make changes, you need to justify your choices to support that your research is relevant, reliable, and representative. One article I wrote was consistently being rejected by one reviewer in particular. In the end, his basic theoretical beliefs were different than ours (I had a cowriter). Because of these differences in beliefs, he would never accept any of our published material/methodology. We were pushing a new view of an established theory. However, we did realize in the first and second revisions that we needed to address the need for a new perspective and method of analysis for the readers or many would have the same reaction. We had to demonstrate first that we understood the prevailing theory and then present an argument for looking at it from a different angle. This way, the audience would not evaluate our article as being uninformed, but rather a new perspective (which they still might have disagreed with). In the end, our revised justifications for our methodology and the basis for analysis convinced the editor to publish over the opinion of the reviewer. It also helped that the other two reviewers changed their opinions about the article so that by the 3rd revision, they were strong supporters for publishing the article.
Once you have written a description of your process(es), it is important to include analysis. New writers and researchers in particular, are adverse to presenting their own interpretations. As a result, the body of a report, dissertation, article, paper, or even book becomes a compilation of facts. It is difficult to realize that feedback may want more of your educated opinion based on your analysis rather than more facts. I see this often when reading articles written by practioners or graduate students where they may not have ever been encouraged to draw their own conclusions. Going back to communication/rhetorical theory, you need to make a claim in your writing. This can be a conclusion, observation, hypothesis, or theory/model. Without the claim, your writing only is descriptive or data. If the feedback you have received includes questions such as "what does this mean?" or "how is this relevant", you have not made a strong enough claim. Likewise, if you have been asked to cite one of your own claims, then you have not made it clear to the reader that this is your claim based on your analysis. Even seasoned writers have this difficulty and you need to take possession of your original ideas in your writing.
Another related problem is supporting your claims. While you may have good reasons for making your claims, most readers will need to be guided through your thought processes for a claim. It is not enough to make a claim and follower up with data in a table. Rather, you will need to point out relevant data and how that supports your claim. If you have feedback such as "Why is this relevant?" or "Can you support this?" (even though you have listed the data), you need to work on explaining how data supports your claim.
Another aspect of revisions of the body is choice of visuals to support your written analysis. I was reminded of the APA guidelines that visuals must be relevant and augment, not replace your writing.
As the Purdue OWL says:
Visual material such as tables and figures can be used quickly and efficiently to present a large amount of information to an audience, but visuals must be used to assist communication, not to use up space, or disguise marginally significant results behind a screen of complicated statistics. Ask yourself this question first: Is the table or figure necessary? For example, it is better to present simple descriptive statistics in the text, not in a table.
Don't assume reviewers won't look at your visuals and tables. Often they will ask you to reformat, add, or delete information that is not necessary. I had to simplify a model I had for my dissertation because it was too complex to follow. Instead, I broke the model up into smaller components which my readers found easier to follow. Of course, sometimes if you have word/space constraints, your first inclination is to put everything into one visual. It is better to simplify so there is a general visual and leave the details for your text when you can relate it to your analysis. Another possibility, if you want the data accessible, is to set the data on a website which you can give readers access to through a note. On the other hand, sometimes a visual will allow you to cull full sections. I just read a revised article that used a visual to explain the various variables used in the study and their relationship to each other. The original version had the explanation in the text which covered 6-7 pages. By the end of the section, I was confused as to how the complex research all related to each other. The one visual allowed the author(s) to cut this section down to 2 pages with a visual, which gave me a better understanding of both the complexity, relationships, and structure of the study.