Posting my Doctor Who theories for the back half of series 6.
The red car that the Doctor reclines on from “The Impossible Astronaut” is a TARDIS
The chameleon circuit broke in the very first serial, but who can say that it wasn’t fixed at some point after that, with all of the consoles regenerating. I don’t think that Amy even knew that there was a chameleon circuit, so when she helped reboot the universe, the Doctor’s TARDIS-that-has-a-broken-chameleon-circuit may have become Amy’s TARDIS-that-is-completely-normal-and-functional-in-every-way. There is precedent for the Doctor to keep something that he likes working on the TARDIS, when it technically isn’t supposed to work that way (i.e. the handbrake). After X-ty number of years with it as a police box, I’d probably get attached to that form as well.
It doesn’t even have to be the Doctor’s TARDIS. There’s the Silence TARDIS and the TARDIS remains in the Bubbleverse.
“A Good Man Goes to War”
Who is the good man? The obvious choice is the Doctor, but he does not consider himself a good man. Who does that leave, Rory? He is a nurse, almost the perfect definition of a good man (well to a human. Sorry, Strax. You will be missed). But the real question is, does Rory have cleanly defined rules?
Which War? “A Good Man Goes to War” had no war. It had a battle. One battle. One battle is not a war. Is the war mentioned the Doctor-vs-Kovarian war or the get-Melody-back war. They overlap but have entirely different motives behind the actions on both sides.
What does Moffat mean by “goes to war”? Is it goes as in “travels to a place of battle”, or goes as in “wages a campaign”? We had traveling to multiple places of battle in the mid-series finale: the Battle of Zarathustra, the Slitheen Crime War, and the Battle of Demons Run. We also see the first hints of the Kovarian campaign, a great big plot thing with armies against the Doctor.
Running
Leap here, but what if, in true Moffetian fashion, a seemingly innocuous bit gets twisted into importance. We have the “Watch us run” voice-over from SitL/FotD. The Doctor talking about how he’s been running for a long time in Impossible Astronaut, and now the Doctor pretending to and Lorna Bucket actually reminiscing about how they ran in the Gamma Forests in GMGtW.
Voiceover
River’s voiceover poem in A Good Man Goes to War is being read to CAL and the children from Silence in the Library. It’s an idea. I’m just putting it out there.
Flesh!Amy command signal
The offhand mention by Rory about how the Flesh command signal could reach inside the TARDIS from “Good Man Goes to War” will eventually come back to bite them in the butt. That carrier for the signal will be the one that was used to hijack the TARDIS in TPO.