My opinion is, no, the mummy discovered is not Nefertiti. Though some of the topmost experts, such as Kent Weeks ans Zahi Hawass have not pointedly denied the possibility, they have brought forth the simple point that the tests performed and the analysis made on the highly cavalier Discovery Channel was nowhere near infallable. It remains as likely as not that the mummy is not that of Nefertiti.
That same episode, in digging into the supposed history of Egypt and Nefertiti herself, displayed dozens of historical innaccuracies.
Assuming Nefertiti ruled after Akhenaten's death, the mummy discovered would not be the proper age. It was claimed she was 25 years old, when recent research is placing her between 16 and 20. There were many royal women from the appropriate period buried in the royal necropolises on the West Bank at Thebes, now Luxor. Those from a specific line of a royal family would look very similar, of course, especially considering how prevelent interbreeding could become.
They claim that the wounds the mummy had suffered somehow proved her to be Nefertiti. In fact, quite often, bits of wealth were placed within a mummy's body caveties, leading tomb robbers to break limbs in order to remove them. It was indicated that mummies with bent arms is, apparently, something unique to kings in ancient Egypt. Well, for one, there was only one bent arm. And many non-kings have been found in such positions.
The 'royal wig' that many cite as proof of Nubian royalty was found near three unidentified mummies, two women and one boy. Beyond that, the workers who were with Fletcher during the discovery deny even having seen the wig at all. The double piercing of the earlobes used to cite Nubian female fashion was actually quite popular among the mummies discovered in the New Kingdom youth.
Beyond all of this, the individual who claims to have discovered and identified the body, when in fact she has done neither, one Joann Fletcher, obtained her degree a very short time ago. Who would blame someone for wishful thinking?
In the end, Fletcher broke the SCA's code of ethics, by creating false evidence to support her claims, and they've suspended her research for it.
We have to be careful of these huge media exploitations. The moment tiny innaccuracies become accepted as gospel, it grows like cancer. Next thing you know, it's in a textbook where 'theory' becomes 'fact.'