Well, for me it looks pretty much nailed on that Miles was also born on the island. The most likely candidate to be his father would be Chang, we saw a kid of his back in the 70's with Dharma at the start of episode 1.
It seems like whatever the effects are of the travel, they effect those that have been there longer. I'm guessing both Miles and Charlotte have been there for like a couple of years or maybe just a year as a child. Because Juliet has been there for more than the few months that the 815'ers were, it's now taking effect on her but Miles and obviously Charlotte were effected first.
I'm guessing we're going to find out more about Rousseau and why she killed her science team in the forthcoming episode, I hope so anyway.
The nod to ajira airways ARG was cool. It does seem like that will be the airline that gets them back to the Island, but how? In that same flash, the camp was a wreck and then folk were shooting at Locke and co. I wonder who it was? The others? I had a strange feeling it might be the 06 and other 815'ers because it seemed so purposfully impossible to make them out but it doesn't make much sense for it to be them.
Didn't suprise me Ben was behind the case against Aaron. Though for a horrible moment during the episode I thought maybe Sun had manipulated the situation and she was the one doing it.
It seems to me like everything is coming together and the next few episodes are going to answer a lot. I'm glad it seems like the 06 will be back around mid-season time, though, because there's still half a season of madness to come!