Nobody has ever done that. You are attacking a strawman. And again you are conflating two separate issues: common descent and the explanation of innovation. Phylogenetic analysis shows that data are organized in a nested hierarchy (which you also misunderstand as “similarity”), for which the only plausible explanation is common descent. From common descent one can infer that a number of transformations have happened, but that alone doesn’t explain how the transformations happened, though it can often tell us what intermediate forms have been passed through.
You are demanding from phylogeny something it doesn’t do and has never been claimed to do, and then rejecting it when it doesn’t do that. Is that rational?