First off, I felt Susan was very badly served by the story. I did not think that her credulity in dealing with the aliens, and her naivety in going behind the back of the government, and then her swiftness to change sides against the aliens, were very believable for someone who has supposedly had her experience of travelling with the Doctor, being married to a freedom fighter and being a political activist herself. Essentially the plot is about her making a pretty huge mistake and the Doctor then rescuing her (and the Earth) from its consequences, and I don't recall that happening in any of her TV stories.
I also thought that the way she and the Doctor treated Alex at the end was equally infantilising. Sure, parents and grandparents do sometimes treat their 17-year-olds like that, but the Doctor at his best is about emancipating his companions and letting them achieve their own maturity. It is extraordinary to have this out the same month as the end of Lucie Miller's story in Death in Blackpool.
The scene with the lunar settlers coming back was a bit underwhelming.
Finally, I'm afraid I didn't think Jake McGann was really up to it. He may well be a fine up-and-coming actor in his own right, but I wonder if (like John Barrowman) he finds it difficult to perform in the recording booth. In a couple of the crucial scenes he sounded rather like he was reading the lines in rehearsal.
Having said that, I thought that Leslie Ash and Carole Ann Ford did very well with the material, and the reunion scene between Susan and McGann's Doctor was excellent. (Even though McGann was unaware of the back-story.)
As for Gallifreyan / human interbreeding? I detected a couple of hints that Alex is not Susan's biological son, but adopted from a human mother. There were a couple of other lines pointing the other direction, but I thought the hints towards adoption were stronger. It was, however, unambiguous that Susan is the Doctor's grand-daughter in Gallifreyan terms (though of course one can speculate about what those terms might be).