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I am experiencing conflicting reviews with my manuscript that recently received its reviews. The reviewer #1 wants me to delete the analysis X for the clarity and focus of my MS, while reviewer #2 wants me to further discuss the results of analysis X, as it appears to be interesting for him/her. Both comments have important points. Reviewer #1 will make the MS short and clear, while reviewer #2 will make the MS longer and open more discussions.

What this means to me is that Section X needs to be revised.

Reviewer #1 is pointing out that section X is not well-motivated as it stands -- because they can't figure out it's relation

Reviewer #2 is pointing out that section X is not good enough as it stands -- because it doesn't address relevant issues about X.

Thus, the two are not necessarily opposite. Reviewer #1 is telling you that you need to better explain why X is as state if you want to include it. Reviewer #2 is saying you need to better address what is at stake in X but recognizes X is significant.

When I get this sort of review, I rewrite that section to make very clear why discussing X matters to the paper (thus addressing Reviewer #1) and try to improve and focus my arguments so that it really answers the objections raised related to X (thus addressing Reviewer #2).

I'm in philosophy, so maybe this advice doesn't apply to your field.

Although this seems like you are stuck between Scylla and Charybis it isn't that bad. It is annoying that the editor is unhelpful, but they are often non-committal in these situations.

Remember that when you send your resubmission with a response to the reviews, each reviewer will see the other's comments. So, in your response, include a section titled "Consideration of reviewers #1 & #2 comments about Analysis X". Explain that both reviewers had good points. And after careful consideration you have decided to do ... whatever you decide.

Depending on the journal / field, one option is to move an expanded version of the analysis (satisfying #2) to the supplement (satisfying #1). If supplement is not available, you can at least put that analysis into a subsection, clearly titled, so that readers (and #1) can more easily skim/skip that subsection without disturbing the overall flow.

I always lean toward including more rather than less, so I would probably end up saying something to #1 like "Based on the thoughtful remarks from reviewer #1, we realized that we failed to clearly explain analysis X, since we, and reviewer #2 both think it is important. As such, we have re-written this section emphasizing how it contributes to our main conclusions."

I have never heard of a reviewer rejecting a paper because an extra analysis was included. If the paper is too long after being accepted, the editor will ask you to trim it down and that can be another opportunity to move things to supplement/appendices.