I've not seen any reviews beyond a couple on my flist, but from the viewing party I was with, it appears the jury is very much out on whether Matthew Graham has redeemed himself, five years after 'Fear Her' was greeted with almost universal disappointment. I thought it was very good indeed; I was more tense than I have been this season, with my hand in front of my face in anticipation of the next revelation or piece of body horror... or perhaps I'm easily scared.
This story seems to be a keystone to the arc. The Doctor's line about fish and chips was a diversion; he'd already decided, I suspect, to travel to the monastery-factory at a point crucial in the development of the Flesh. He has been studying Amy's quantum pregnancy for the last few weeks, and rejecting options - hence the "It's not like that at all" asides. I speculate that the Amy who is travelling with the Doctor and Rory is made of a more advanced version of Flesh, hence the Doctor's reference to 'early technology'. The original Amy is still 'driving' the copy, unconsciously; when she wakes up (and sees the Eyepatch Lady), her conscious experience overlaps with that of the copy. Though the copy is not pregnant, to some extent her body is reproducing the symptoms of pregnancy, or whatever link across time and space the two have is causing the TARDIS to report on both Amys at once.
The implications of this for Rory would involve a lot of emoting next week - Jennifer has shown herself a potential focus of jealousy for Amy, but what if Amy is herself an 'imposter'? This would call Rory's sympathy for the duplicates into question, as well as turn Amy's rejection of them as 'monsters' on its head. (A lot of us suspected that everyone left of the monastery team after the Doctor, Amy and Rory awake is a Ganger; we will, I expect, come back to the sneezing character again - will he cough up Flesh?)
Just possibly, I wonder whether Flesh has some connection to the origins of the Silence - their tones are somewhat similar...