Not sure what you mean by "completely objective." Molecular data is of course not infallible. I cited several instances in which the choice of outgroup really affected the reliability of the results. That said, molecules do offer something morphology has been unable to accomplish and may never be able to do so. For example, it would perhaps be impossible to answer the question of exactly how closely related the Neandertals are to living human populations. That answer finally came when mtDNA data became available for living human populations and from a piece of Neandertal bone.

Further, until recently, it is nearly impossible to know where a speceis such as Lampropeltis zonata or Charina bottae had originated. mtDNA shows that both originated in southern California and migrated north. Even more revealing is molecular data on the western skinks. Long considered to consist of but 2 morphologically distinct species (Eumeces skiltonianus and E. gilberti), it turns out that the gilberti morph has arisen independently from different populations of E. skiltonianus, even though the different gilberti morphs may interbreed freely with one another while being reproductively isolated from the parental skiltonianus. It would have been nearly impossible to reveal such complexity without molecular data.

You have also mentioned the lumping of species using allozyme and mtDNA data. I think that practice is untenable. Species consist of sets of actual or potentially interbreeding populations, and no mtDNA data can possibly tell us anything about reproductive isolation. To this date, we still do not know whether Neandertals are reproductively isolated from modern Homo sapiens or not. Hence the question of whether Neandertals and modern humans are the same species remain an open question.

There is no doubt about it, the study of phylogeny is best done with molecules, simply because there are so many more molecular characters than morphological ones and because many molecules are selectively neutral whereas morphological characters tend to be adaptive and therefore more likely to be the result of convergent evolution. Nevertheless, phylogeny per se really gives us an incomplete picture.

I have taken part of an actual branching diagram from a published paper. This tree is constructed from mtDNA data. Can anyone tell me how many species are represented in this tree? I seriously doubt that anyone can figure out the answer since mtDNA data can only give us information about lineages, and lineages are not species. The result will be revealed in a future post. Have fun in the mean time.

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