How to negotiate with referees of your paper I have submitted a paper several years ago and its referee process took about three years and I had to revise the paper six times to get the final approval. The paper had two helpful and knowledgable referees and I appreciate their comments and suggestions, but I have also had the following problems with their suggestions:


sometimes their comments contradicted each other. For example, one of them wanted me to add a discussion and when I added that part he wanted me to remove it in the next revision. 
they often wanted to expand the scope of the paper, but due to some technicalities I had to consider some restrictions to get the expected result.
they gave me new comments and proposed new modifications after every single revision, while they could suggest all their comments in their first report and this made the referee process this long. 
one of the referees wanted me to address some related works in other papers in my paper, which was actually unnecessary.


I pretty much obeyed all their suggestions and comments and finally the paper was accepted and now it has been published. Although I learned a lot during the referee process, I wished I could negotiate with referees and do not have to obey them in every little detail. Besides I had this feeling that I have somehow lost my freedom as the author of the paper during this process and I have no control on my paper any more. I had to do whatever they asked me even if I was not completely convinced it is a right thing to do. I have also had some of the abovementioned problems with the referees of my other papers. You perhaps know that journals often have this policy that you either should implement all the changes suggested by referees or withdraw the paper. This policy leaves little room for negotiation. So my questions are:

An author, in order to discuss his/her points with referees and do not obey some of their suggestions and comments  or ask them to not delay the referee process further, what is the best strategy to negotiate with referees? Is there any diplomatic way for this negotiation or we have to obey referees all the time? Have you ever had similar problems with referees of your papers? How did you overcome these problems?
You perhaps know that journals often have this policy that you either should implement all the changes suggested by referees or withdraw the paper.


Which journals have such a policy?  I don't think this is the case for any AMS, MAA, or SIAM journal, for example, and I'm not aware of any journal with such a policy (although of course I have direct experience with only a small fraction of the journals in mathematics).  Here's how it works in the cases I'm familiar with:

Any changes suggested by the referees are merely suggestions, which do not need to be followed if the author and editor are in agreement.  If the change involves fixing a mistake or correctly attributing work, then no responsible editor will accept the paper until the situation is resolved (either by making the change or establishing that it is not needed).  Matters of clarity are also taken seriously.  However, some referee suggestions are just opinions that the author may reasonably disagree with.

It's perfectly reasonable to write to the editor and say "Here's a new draft of my paper.  I've made changes A, B, and C proposed by the referees, and I'm grateful to them for identifying these issues, but I have not implemented D and E.  I think those changes are not truly needed, because ..."


  what is the best strategy to negotiate with referees?


I'd think of it instead as negotiating/discussing with the editor.  The editor is the one who makes the decision, with the referees providing advice and expert opinions.  Ideally, you'll be able to convince the referees that not all of their proposed changes are necessary, but the editor is the only person you need to convince if the referees are stubborn.

Editors are used to this.  As an editor, I've occasionally written an acceptance letter (conditional on revisions) that says explicitly that only some of the changes are really needed, and even when I don't say so authors certainly don't always make all the changes.