Name's the Same: Until recently, the villain's name was consistently transliterated as Doctor Who but no relation implied to his more famous heroic counterpart (who really is not properly called Doctor Who but The Doctor). No one told anyone differently so it stuck. In fact, at the time of the film's release, The BBC series was mostly unknown in North America. In recent years, the name has become transliterated as Dr. Hu, which assumedly was the original intent. However, this theory ignores the fact that this Dr. was created by American writers for an initially American audience and made his debut in an English-language cartoon.
The fact that the villain bears a slight resemblance to the William Hartnell incarnation may be more than a coincidence.