Okay, so I was thinking about the last two seasons of Doctor Who as I was trying to fall back asleep unsuccessfully this morning. And I noticed that there seems to be a prevalent theme over the past 2 seasons: transformation and/or things not being what they seemed.
Anyway, look at how many times there's been an example of those things (literally or figuratively) over the past two seasons, and I'm probably forgetting some because I'm doing this off the top of my head...
1. The Doctor regenerates from his 10th to 11th form (okay, technically at the end of the New Year's special, but the effects were seen mostly in TEH.
2. Prisoner Zero, a multiform, can take on the shape of anyone who is unconscious in order to hide from the Atraxi.
3. Amy's house has more doors on that one floor than the Doctor says in it. So one door is being hidden for some reason.
4. The Daleks in "Victory of the Daleks" appear to be subservient to humans, supposedly created by Bracewell (who instead turns out to be their creation), in order to trick the Doctor into making it possible for a new Dalek race to be created and the old one was destroyed.
5. Amy in TToA/FaS appears to be becoming a Weeping Angel for a time.
6. The fish vampires in Venice use a perception filter to appear to be human.
7. The whole episode of "Amy's Choice" is nothing but an illusion created from the Doctor, Amy and Rory's minds.
8. In THE/CB, at least one of the miners (or was it two of them?) end out being turned into a weird human/Silurian hybrid. And Rory starts on his own transformation from being the (apparently) meek, let everyone walk all over him, nurse that he was in TEH by sacrificing his life for the Doctor, whom he just a few episodes before told flat out was "dangerous" to the people around him.
9. Craig's house in TL has a spaceship hidden above it with another perception filter type of thing.
10. In TPO/TBB, Rory has been brought back from the dead as a plastic Auton, and later, after the reboot of the universe, is turned back into a normal human being (albeit one with over 1900 years' worth of memories). He also continues on his own transformation from nurse to warrior.
11. The Doctor literally "changes" Sardick in ACC from the bitter old man he was into a much happier one.
12. Amy is replaced sometime between the end of TBB and the start of TIA with a ganger version of herself, which we don't learn until later in the season, I'm just putting it here so that it's in order. However, I'm not sure if it occurs before or after the "Space" and "Time" mini-episodes.
13. The mini-episodes "Space" and "Time" give us doubles (or "future selves" if you prefer) of Amy, the Doctor, and Rory. Oddly enough, this is the only time during the 6th season that there is a duplicate of Rory (robot Rory notwithstanding), yet there are duplicates of all of the rest of the main characters (including River) on multiple occasions throughout the season.
14. The Doctor changes how the Silence (or at least the aliens that we presume are called that at this point in time) are viewed by humanity, so that they will be killed on sight, rather than be able to manipulate them (and I wonder if this wasn't really the first shot, so to speak, on the Doctor's part which brought about that "long, bitter war" with him that Madame Kovarian refers to later in the season. The Silence were sent back to create the weapon to destroy the Doctor, but end up being the cause of the war in the first place. I don't know, but it would be really ironic if Madame K. and company were the reason the war against the Doctor started in the first place.)
15. The Siren in CotBS is first viewed to be a threat by everyone until the Doctor realizes that she is actually trying to help and is in reality a medical program.
14. The TARDIS's self is transplanted into a living, breathing woman.
15. In TRF/TAP, we have a multitude of duplicates running around: all of the acid miners plus the Doctor have one. And everyone still ends out with only one of them in the end, at least among those who survive. Two of them died both as a ganger and as a human (Jenny and that one guy, Buzz, I think his name was). Two gangers survived, one of the original acid miners did, as well as the Doctor. And we finally learn that Amy has been, in fact, a ganger since before the season started.
16. Melody goes from being Amy & Rory's baby to being River Song, the sometimes companion they've known for some time. And baby Melody was also a ganger in AGMGTW. Rory also finishes becoming the warrior, willing to protect his wife and daughter, to the point that he literally takes on a Cyber legion in their own headquarters with nothing more than a sword and a sonic screwdriver for protection (okay, the Doctor had his back, but the Doctor wasn't the one who was running about HQ). And Rory realizes what he's become with the nice juxtaposition of Strax, the Sontaran warrior who became a nurse and died at Demon's Run.
17. Mels, best buddy of Amy & Rory, turns out to be their daughter Melody, aka River, in LKH. We get her regenerating into a new form for at least the second time (first time we know of was as the little girl in New York back at the end of DotM), as well as the apparent start of her transformation from the psycho killer programmed to kill the Doctor into River Song, the one who loves him.
18. The Tessalecta (I think that's how it's spelled) is a robot that can transform into anyone or anything in LKH, and does so on several occasions, becoming a Nazi officer, an enlisted man (and later adding a motorcycle to this guy after Rory steals the one he originally had), and Amy at various points.
19. In Night Terrors, we see both Amy and the landlord guy turned into giant dolls with a touch.
20. There are two Amys, older and younger, in TGWW. The older one has transformed from the young girl who had total faith in the Doctor and has instead grown into a bitter old woman (kind of the reverse of what happened to Sardick, isn't it, earlier this season?) who hates and resents the Doctor and his promises. The younger version is still unspoiled by that, though, I think, is slowly realizing that the Doctor isn't always going to be there to save her.
21. Rory feels as though the Doctor is trying to make Rory into him, and quite honestly, he is. Even down to the glasses that Rory is wearing, which really makes him resemble the Doctor's previous incarnation at times. Moreover, the Doctor is forcing Rory to learn what the Doctor has to do every single day: make the tough decisions that no one else wants to make and live with the consequences. Rory, understandably so, doesn't like have to choose which wife he wants because Rory is a good man who loves both of them. I think, if he was able to, he would have taken both of them home and would have loved both of them equally.
22. Amy completes her own transformation (in part thanks to the Doctor letting her go) in TGC, going from the little girl who would always wait for him to the grown up woman who is married and ready to start a new adventure with her husband Rory on Earth, together. I don't think Amy would have reached this point, however, if the Doctor had not done what he did. Or at least not for some time yet.
23. And the Doctor likewise continues on his own transformation from Time Lord Victorius back to the anonymous guy who randomly shows up to help people out. The Minotaur's words at the end, which he's translating, appear to be talking about the Minotaur's situation itself, but with that last line, "I wasn't talking about myself," it's pretty clear that it's referring to the Doctor. He's ready to make the changes necessary to drop his "godlike" persona because he realizes that he needs to do that, or else more people will end out getting hurt.
I do think it's significant that Rory is the only one who hasn't actually physically been doubled or changed in any way during this season (ie, into a doll), that his transformation has solely been in his mindset. What it means, I'm not sure, other than the vague hope that he isn't the one whom River kills, because he is easily a "good man," much better than the Doctor (who himself states that he isn't a good man)...