One of the most frustrating things that we have to face as researchers are reviews. We all want people to recognize the hard work that went into developing papers and grants. None of us got to the point that we were sending material out for review except by putting in many years and a startling amount of hard work.
So it is very annoying when strange reviews come back. But I have learned that there are a few basic rules:
Should the paper be rejected:
1) Decide if the criticisms are substantive or stylistic. If substantive, then you need to either redevelop the paper or retire it. This is never a pleasant discovery but, in the long run, you'll be glad that a sharp reviewer caught an issue. In my experiences, true substantive critiques are rare.
2) If the criticism is stylistic then don't put time into it. Likely the next set of reviewers will have different preferences. Resubmit rapidly.
3) If the criticism seems to apply to another paper, entirely, then seriously consider rewriting the confusing sections for clarity. You are the subject matter expert -- it is not reasonable that reviewers and readers will necessarily follow all of the nuances.
In the same vein, as a reviewer, asking for massive redevelopment for purely stylistic reasons is often a poor choice. Ask whether the paper is methodologically valid (no point in letting mistakes into the literature) and relevant. These are the real questions that need to be considered.
Peer Review is a frustrating process but it can really improve work if you take advantage of it.