One of the things that I love most about Doctor Who is that plot holes, which are usually picked over by sci-fi geeks, are ten a penny and no-one really cares. One of the biggest from New Who is Jenny, the Doctor’s Daughter, from the episode of the same name.
Jenny (whose actress is actually married to Tennant and the daughter of the Fifth Doctor, Peter Davison) was cloned from the Doctor’s DNA and dies at the end of the episode, but then she regenerates and escapes, never to be seen again.
This episode, where the Doctor gets involved with a war with the Hath, was received with a collective “meh”, but its enclosed story had an Old Who feel and the plot twist was surprisingly unexpected.
The companion competition between Donna and Martha continues and the Doctor monologues brilliantly about the Time War. As Jenny seeks to follow in her father’s footsteps, I’ve always been surprised that the Doctor hasn’t run into this quasi-Time Lord again.