How to respond to an editor's post-review comments suggesting major changes I'm not willing to make? I submitted a paper (in applied mathematics) to a journal about a year and a half ago. I received the first feedback from the Editor in Chief about a year later (the reviewing process for this journal is usually long): the two reviewers were positive and suggest minor revisions (clarification, typos, etc.). At this point, the EIC wrote me that he would keep his comments for the next round of reviewing.

The second feedback came 6 months later. The two reviewers replied very shortly, saying that their requests had been satisfied and one of them recommended publication overtly.
At this point, the EIC wrote a lengthy set of comments on the paper which can be roughly divided in two categories:


On one hand, revision of typos, clarification of some paragraphs, etc., that the reviewers had missed.
On the other hand, he commented on the theoretical framework used in the paper, saying that it was unnecessarily complicated and hoping there would be a simpler way to achieve the same goal. He suggested to cut most of the parts where this theory would be used and to rewrite the paper accordingly.


I feel being in a delicate situation, where I'd like to have this paper published, but not sacrifice its background and the main ideas it implies. For me, the theory which is proposed provides a very simple way to deal with the examples. I am considering writing to the EIC to essentially ask him if he's ok to keep the theoretical background (with justifications from parts of the paper) in which case I'm willing to make the revisions he requested for clarification (I'm considering withdrawing the submission in the other case).

What do you think would be the best way to handle this situation ?
I would suggest the following thought experiment. Take a day (or at least a couple of hours), and fully embrace the editor's suggestions. Think about why h/she made them, and think about how you would revise your paper to fully incorporate his/her suggestions, and in what aspects it would make the paper better.
Sleep on it a couple of days. Then, if you decide you prefer not to take the editor's suggestions, you will be in an excellent state of mind to write a reply.

I carefully considered suggestion X. As pointed out by the editor, this would have advantages Y and Z, and W. [It is especially helpful to not just say the same thing word-for-word, to show that you thought about the editor's suggestions carefully.]
Nevertheless, I feel that for the most part the paper is better as is, for the following reasons: ...