I think you're spot-on about the Abbies. I was thinking the same thing about the female being the leader, and what must be telepathic communication. There is clearly an intelligence to them, to see how quickly they went from appearing to fear fire, to figuring out how to use it to torch the crops. Possibly they never feared it, but had the intelligence to make it appear so to draw the folks of Wayward Pines outside the walls comfortably!
Megan (wheelchair lady) is at the heart of everything wrong with this place...it will be interesting to see how the Doc interacts with and/or corrals her as the new head of Abby research. To that end, though, I wonder if the Hitler-wannabe kid leader (forget his name) is really running the town, or if its really his girlfriend running the place. Sometimes it seems she is more in control of events than he is. Looks like I was right about the Doc's wife (ex-wife now?) being a bigger player in all of this, too, finding out she's the architect of the whole town.
Also...thinking more about Ethan's wife since the character doesn't seem to be going away. Who wants to bet she ends up with the Doc at some point, now that the Doc's wife has re-married in the Wayward Pines timeframe?