At one point I was noticing that it was taking a while to get in to the meat of the story in this episode, but I think that was the idea. It was a year that they had to wait to figure out what the cubes where, and as to many shows do, you can't rush by a year in 15 minutes.
The Ponds discuss the need to make a choice between real life and their ten years of Doctor-life. Every turn they're shown that while they enjoy Doctor Life, if they`re ever going to live this life they need to do so, and not cling to him, like an addict to their dealer.
Dialogue for this episode:
Rory: There couldn't be life forms in every cube, could there?
Doctor: I don't know, and I really don't like not knowing.
Doctor: Since when does science run the military?
Kate Stewart: Since me.
Kate Stewart: Science leads, he always told me. He said he learned that…from an old friend.
Doctor: We don’t let him down.
Rory: What do you think we do when we are not with you?
Doctor: I imagine mostly kissing.