miRNA is best for studying epigenetic regulation of gene expression. RNA , specifically mRNA gives information on genetic status of the gene being expressed, but is not easy to assess and so the mRNA is first converted to cDNA which you can amplify to assess mutations or sequence to assess mutation that may have been present in the original mRNA. If mutation is at the genomic DNA, then it is best to assess this by DNA sequencing. Because the genomic DNA has more genetic information than the gene expressed, finding specific primers to assess genetic status becomes a challenge.
In other words, the best approach may be the one that best answers the information you are trying to find.
It depends on the organism to be studied. If the genetic information is under control of RNA (as HC viruses) then RNA is important for mutation study. In higher organisms DNA is totally responsible for controlling traits. In later case, DNA has importance for mutational studies.
I think RNA is better to investigate certain mutation as it reflect genne expression only, but DNA structure contain both exons coded sequece and interones non coded sequences.