Doctor Who: 10 Dropped Plot Threads We'll Never Get The Answer To
2. Is The Doctor Half-Human?
Here's a sore point for many fans. 1996's UK/US co-production Doctor Who: The Movie attempted to kick off a new series with Paul McGann. There were lots of major concept changes planned but the only one that made it into the finished TV movie was the revelation that the Doctor is actually half-human!
As this has never been mentioned before or since, fans like to hand-wave it away as just something unique to this regeneration. However, the dialogue that establishes this fact is very clear that this has always been the case. The Doctor even says he's human "on [his] mother's side."
Russell T. Davies is one of those who's not a fan of this Spock-like backstory and almost wrote a joke in 2008's 'Journey's End' that would have explained the half-human thing as "a 24-hour bug", suggesting it wore away after the Eighth Doctor's first day. However, he ultimately cut it as he thought it was too fan-orientated.
As things stand, then, the only evidence on the matter says that the Doctor really is half-human. Unless the Thirteenth Doctor proves otherwise.