Unfortunately, the mtDNA cannot prove that Neanderthals are their own species. Some of the reasons for this are as follows:

Scientists do not know what the original mtDNA sequence was; they are using the mtDNA as a molecular clock in order to determine the divergence of Neanderthals and H.sapiens. The mtDNA does not have an entirely uniform rate of mutation thus giving only a roughly approximate coalescence time. Many would argue that mtDNA cannot be used as a reliable molecular clock at all.

Remains from lower latitudes or older samples have poor organic preservation. The gene products of mtDNA are amino acid assemblages which undergo furthur modification to form the proteins encoded by mtDNA. It is the amino acids in these proteins that undergo racemization. In nature all of the amino acids are in the L-confermer. After the death of the organism, through a process known as racemization they convert at a steady rate to the D-confermer. High ratios of D:L amino acids are indicative of poor preservation and therefore cannot be used in analyses as a reliable sample.