How far should you go in compromising your work to get it published? To get my first paper published I carefully followed all reviewers’ instructions as I was convinced that reviewers are experienced researchers and reviewers. After major revision my first paper was smoothly accepted. 

However, as I progressed in research I also grew to dislike my first publication. Following the reviewers’ instructions made the paper unbalanced and disrupted the line of reasoning. That is because many reviewers request additional changes reflecting their area of expertise, but not necessarily contribute to the original objective and scope of the paper.

I also learnt that ‘the academic standard’ is a broad interpretation depending on the reviewers’ experiences and preferences. Also reviewers make mistakes in their judgement. As I was quickly asked to review myself, this blog greatly helped me in identifying my own mistakes: https://sites.umiacs.umd.edu/elm/2016/02/01/mistakes-reviewers-make/

In following publications, supported by my experienced supervisors, I learned to refute more. Even if I want to compromise, my supervisors will object because it is also a matter of our long-term reputation. The flip-side of the coin is that reviewers get pissed-off because no one likes a rebuttal, no matter how politely and respectfully it is written. It just provokes a response in reviewers to legitimize their views and invites additional scrutiny of my work. 

I do however fully agree with my supervisors. It is a balance between short term targets and long term success. It is in essence a matter of personal integrity. But it is also personally stressful and it takes a lot of additional time and effort on the expense of research. I often think, just let us compromise and get the work published smoothly.

How should I deal with this dilemma? Have others had similar experiences?
When I started writing papers, my supervisors advised me that I should consider the reviewers' comments and suggestions but not be bound by them. When revising papers after reviewer feedback I would write a response letter addressing each point, whether I had incorporated the reviewer feedback or not, and importantly - why (or why not). In most cases I found that the editor considered a justification for not amending (a portion of) the paper to be acceptable.

In one case a reviewer wanted what amounted to a literature review of possible alternative solutions, which we considered to be far beyond the scope of what we were reporting in the paper and we ultimately withdrew the paper and submitted it to a different journal.