But remember the Doctor's face in this scene. He is not overjoyed at the reunion. He is shocked at what his companions have become. Martha Jones, willing to destroy her race to save the Universe, just like the Doctor. And Rose Tyler, cheering it on.
And there goes my heart. Remarkable how only one sentence can make you sad------->I took this as a joke on Clara's height, u mean the doctor said that in those moments he missed Amy because she had long legs.