It's the first half of a two-part story. As a very intense story I'm sure the second half is going to be amazing and even more intense.
The Doctor is taking a very strange strategy here. At the very beginning his screwdriver tells him "near people" are approaching, so therefore he sorta knew going into the situation that they'd be meeting artificial people. And then he's introduced to the machine they use to generate the artificial people, it's a vat of this "Programmable Flesh", and he gets psychic communication with the Flesh. That psychic communication tells him something, that this Flesh is "alive" for some definition of alive. And then from that point he's interested in helping these Flesh Creatures to find a way to survive and live.
In previous Doctor Who stories he's often acted to help any life form he comes across, especially newly created life forms. This case fits the pattern of technology creates a new form of life, and he works to protect the existence of that life form.
Whereas a typical human might look at this and see - an artificially created being that doesn't have the same right to exist as "real" humans.
The Doctor's attitude strikes me as similar to when they were with the Homo Reptilia (Silurians) last season, and he tried to engage in diplomacy between warring camps but it all goes to hell making a war.
He says "this is only flesh, the early stages of the technology". In other words, he knows about this technology but I can't recall seeing anything like this in earlier Doctor Who. That is, unless this is an early form of the Nestene's (a.k.a. Autons). When confronted on what he knows about this he refuses to answer.
If this is an early form of the Nestenes then it's interesting that Rory falls for Jennifer, one of the dopplegangers. Rory, as a former Auton, might have quite a bit of understanding for plastic people.
There's a strong connection in this story with Blade Runner .. in that story the "Replicants" were given memories of lives they had never lived so their bodies would feel more at ease with living, but that left them yearning to find the life they never lived. Similarly these dopplegangers think they've lived the lives of the humans who are animating them, and then when the gangers take on life they have delusion that they are the real person ... but are they? Is it life or is it memorex?
Coincidence? In Review: Doctor Who S06E04: The Doctors Wife the main word was "Alive". It also featured a machine who formed sentient thinking patterns (the TARDIS). Hurm..
Who's this borg eyed woman in the alternative universe playing peekaboo? Why does the Doctor keep checking on Amy's pregnancy? Why is there doubt about the pregnancy?
Now... at the end of the episode we learn about .. there's a new Doppleganger version of the Doctor. That's creating a question of who was the Doctor they met at the beginning of the season and saw killed. Was it the Doppleganger Doctor or the Real Doctor?