"The system of nomenclature is independant of methodology."

Quite correct. A cladist can, for example, recognize paraphyletic taxa, as a few of them have done. But these cladists are viewed with suspicion, as Mayr and Ashlock point out, by other cladists. Conversely, a systematist may adhere to Hennig's classificatory practice by recognizing only taxa consisting of one ancestor and all of the descendants of this ancestor even though his/her tree is based on distance data, which is categorically rejected by the cladists.

I am not referring to tree building or interpretation. I am referring to the fact that different taxonomists can classify animals quite differently even when both are basing their classification on the same tree or set of phyletic relationships. A taxonomist who tolerates paraphyletic taxa, for example, may recognize a paraphyletic Clemmys for the 4 North American species of emydid turtles, whereas a Hennigian may splinter the 4 species of Clemmys into two or more genera. This is the case because taxonomy is independent of systematic methodology.

"Exceptional cases while interesting do not help the majority of science."

Science is based on the accumulation of facts. Every little bit helps.

"Also one of the biggest difficulties with cladistics is weighting. If you sequence a gene and come up with several hundred characters and then combine it with a morphological annalysis with say 50-100 characters you have a weighted and biased dataset, biased to DNA as it swamps the dataset. Geneticists argue that the morphology should be excluded altogether and later mapped on to the gene sequence trees and that fossil evidence should be excluded altogether as well.
Personally I call this manipulation of data."

Character weighting is a problem for systematists in general, not just cladistics. Darwinians argue that the cladists who weight all characters equally are just as subjective as one who gives each character a different weight. Clearly, some characters are more informative than others. For example, the way a turtle retracts its neck into the shell cannot possibly be given the same weight as, say, whether its plastron is hinged or not. Character weighting is therefore necessary, but it is not easy.

I agree that there is no justification for ignoring scientific data. Molecular trees can be corroborated with morphological characters and vice versa. I am not sure the practice of dumping all the molecular and morphological characters into the same dataset and finding the shortest tree will give a better result. It all boils down to the goodness of the characters, not whether they are molecules or morphological characters nor how many characters one uses. Given good characters, just a few of them will suffice. For example, the SINE characters that systematists used to link artiodactyls with whales, though few in number, have been very informative of relationships.

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