Why is there a dispute about cis and coding?

There has been a fighting in the evolution field about the molecular genetic mechanisms of evolution, especially evolution of morphology, in the recent years. I got involved because I have no choice.

As is known historically that proteins come from the coding regions of a gene, it's also known for long that changes in the nucleotides in these regions would result a mutation if it changes the meaning of the codon. The textbook I learned when I just got into the biology field clearly said: there are several types of mutations; insertion and deletions (not multiple of 3) will cause a frame-shift which is really bad, substitutions can change the meaning of the codon or just stay neutral. At that time, I have no idea that changes in the cis-regulatory region would matter.

Now I read about evolutionary-developmental scientist (Jacob and Monod 1961) who started the idea that evolution can be mediated or even mainly dependent on changes in cis-regulatory region for evolution of this specific phenotype -- morphylogy. One of the main leaders on this side is Sean Caroll from UWM. Such an "assumption" of course make the conservatives unhappy. People started standing up one after the other to disagree. There are even papers point directly at every sentence said by cis-regulatory scientists. A notable example is the hoekstra and coyne 2007 paper. As the heat generated by the discussion increases, people can not stay silence any more and had to stand up to clear up for both sides: the Stern and Orgogozo 2008 paper, titled "The loci of evolution: How predictable is genetic evolution?" Which really helped to cool down both sides, I believe.

But to me, of course I believe cis-regulatory changes play an important role during evolution, but this does not necessary exclude the idea that coding mutations are also important. Why do you need to place cis at the most important position? Why do the other need to treat cis as nothing? Why one of them, cis and coding, have to win? Why do we care which side wins? Why should we waste time on such a dispute? It is great to learn that functional mutations can occur in the cis-regulatory regions, in addition to what's known for a long time that functional mutations happen in the coding region. If there are additional mechanisms, scientists should be very happy to learn as well. It is like, if you have two child, why need you know or try to prove that David is the best and Jack is the worst of your children? It's true that such discussions would help to sharp peoples' ideas and make people think more carefully. Except for that, I still think we doesn't need to use one mechanism to conclude everything. Yes, reductionism is important to science, but please don't be too reductive...