How to respond/reply to a reviewer who doesn't seem to "get" the paper
If the referees -- especially more than one -- are not "getting" the paper, then there are just a few possible reasons why this can happen.  In order of least like to most likely:


The reviewers are not expert enough
The author is submitting to the wrong journal
The author is not telling the story well enough


The first is rare, but not rare enough.  The third is very common.

The proper response to the first two, but for different reasons, is to resubmit elsewhere.  For the first, you'd be looking for a journal with a better referee pool.  For the second, you're looking for a more appropriate audience.

The proper response to the the third, bluntly, is for the author to write better.