Mtdna, shows relationships, exacting. Its measurable. Scale counts are something measurable. Color and pattern are neither,
Dna is solid written in stone(in their bodies) Scale counts are part of their body, color and pattern change with the winds.
I am not a big fan of Mtdna yet, but I will be once they make it useful to the casual herpers like us. YOu know, when you pick up a snake and ask, what the heck is this. Once it can do that without having to research many papers, I will like it.