You might want to look into the history. The genetic data is a relatively new thing. Before then and before cladistics, taxonomy was based on morphology alone. Not just the skeletal structure but the soft parts, too.
When an earlier discussion focussed on the skeletal similarities between the wolf and the thylacine, one thing that cropped up was the teeth. Wolves have distinctively canine teeth. Thylacine teeth are quite different. They really are easy to tell apart if you look at dentition.