[ahayes]

I think it's more accurate to say that no significant interbreeding occurred.

As for the use of contemproary mtDNA, I disagree that the differences would be trivial.

Upon what basis?

[From many - one.]

Real timeline is too short. According to this website:
http://wwwrses.anu.edu.au/environment/eePages/eeDating/HumanEvol_info.html

H. sap and N. nea co-existed 100,000 years ago in Israel with a common stone industry. That would have been highly unlikely without interbreeding at that time, when the two groups were probably less differentiated.

Generally differention of a species into a new environment encourages significant diversity, later pruned as the niches fill up. The 20,000 years from then til now could very likely represent a significant selection effect, thus makng us more different from H. nea now, than our ancestors were then.