... but i'm so tired I can't think straight anyway, so I thought I might as well add my crackpot / exhaustion induced theories to the pile.
I watched The Rebel Flesh again the other night and remembered some of the stuff I forgot to put in my original post.
ETA - I refer to the synopsis for ep 7 in this
The Doctor clearly had the intention of heading off alone to investigate the factory/monastery and I don't think it was just because he wanted to protect Amy's unborn possible-baby. I mean, if he was that desperate to protect him/her, he'd have sent her home by now, no?
More pregnancy scanning (yawn) and a reappearance of "eye-patch" lady. Back when she first appeared and said "she's still sleeping", I started to wonder if what we were seeing was really a dream that Amy's having. If it's a drug-induced one and she's sedated, eye-patch woman could be appearing as she starts to come out of it - and the hatch slams shut as the drugs kick in again.
This would fit in with the blurb for ep 7 - Amy Pond has been kidnapped, wouldn't it? She was kidnapped back in DotM and replaced with a Silence-made "Flesh" copy, only this is a more advanced version and able to remain stable without proximity to the original. That would also fit with what the Doctor muttered about the version of the Flesh they encounter at the factory being an "earlier" one.
And if the "kidnapped" storyline is what starts ep 7, that would mean the Doctor finding out about ganger!Amy - or having his suspicious confirmed - in ep.6. Which would tie in with what Matthew Graham said about getting to write two cliffhangers. (One at the end of each episode.)
The real Amy IS pregnant - but the Flesh copy isn't (or vice-versa I suppose) which accounts for the inconclusive scans. I don't, at the moment, have any theories about the possible!baby, although I do think that the idea of some Rosemary's Baby type scenario relating to the Silence or some other alien species would be going a bit too far down the horror route for a family show.
Are the workers at the factory "real" at all? The gangers that we've seen have all the memories and experiences of their originals and believe themselves to BE the originals. So what's to say that the ones we believe to be the originals aren't gangers, too?
The missing hour. A lot can happen in an hour - enough time for the Flesh to clone everyone, so the Doctor, Rory and Amy we've been seeing since Eleven fell off that tower (you'd think that he'd have learned not to climb tall buildings during electrical storms by now, wouldn't you?) could be gangers.
Is the ganger!Eleven we saw at the end of TRF the only one in existence? What if there are two copies - one good, one bad and it's the good copy in the spacesuit at the beginning of TIA?
If the only way to kill a Time Lord is to kill him before he can regenerate; and, as I'm led to infer by Eleven's discovery that ganger!Chris Skelton (sorry!) had a heart - gangers are exact copies, that ganger!Eleven is also an exact duplicate... then that's the only way he could be killed, too. But it's too obvious, isn't it? That THAT is the version of Eleven who's killed by the lake in TIA? And that he's killed by another doppelganger. (And then what happens to that doppelganger? If they're exact copies, can they regenerate, too??)
I know that there's been much trumpeting about the mid-season cliffhanger being a "gamechanger" and that something will happen which will change the relationship between the Doctor and Amy forever. Personally, I'm hoping that means she's going to bugger off.
But I hope that, even with what is surely going to be a cliffie of MASSIVE proportions, we're going to get some answers, too, otherwise the three month wait is going to be pretty unbearable.
One problem I'm having with this series so far is that the "arc" episodes (Moffat's two) have contained SO MUCH information (and undoubtedly, so much misinformation) and left so many hanging threads, that I'm worried some of them will get forgotten. DotM asked far more questions than it answered, and I really hope that this isn't going to be the case with A Good Man Goes to War. I want something to come back to in the autumn, but is it too much to ask for a few of the hanging plot-points to be resolved before then?
I'm about to take a nose-dive into the laptop, so I'll stop there although I'm sure I've left something out. I'd love to hear your theories, too - crackpot or otherwise :-)