What I liked most, aside from the things you've named, was how subtly they put in their "parents should love and care for their children" message. You had Clara's employer, starting out as distant and unable to relate to his children, to him hugging them both to him at the funeral. I thought that was nice and downplayed, yet got the point across.

Madam Vashtra and Jenny are Holmes and Watson, the originals, and Arthur Conan Doyle is using their adventures as his inspiration. (Couldn't resist that one, Moff, could you? Well, I'm all for it.)

I wondered if it was a small swibe at Elementary - both Holmes and Watson being women, and a married couple at that - but there didn't seem malice in it, so it was fine. Besides, Jenny and Vastra!

I'll also have to hand in my geek card, because I couldn't decide whether the Great Intelligence was voiced by McKellen or Patrick Stewart... *facepalms*