Looks like there are two time skips. One is coming up soon (2 years) after Saki and Satoru return to the village. Another 12-year time skip is also going to happen later on.
There is some homosexual content coming up (may be toned down in the anime), including a sex scene between Shun and Satoru, and maybe a sex scene between Maria and Saki. Doesn't really bother me but there it is, any homophobic folks might as well drop this show now even though I doubt they'll be very explicit about it in the adaptation.
And, as was hinted at in the anime already, it seems that Saki had sex with her mom (whatever that means, I don't really wanna go there). It's some kind of teaching thing but technically it's incest.
The kids are going to recover their Cantus abilities "very soon", apparently. I hope they do that in time to kick some bakenezumi ass
They also get to keep the information they learned from the librarian and it'll play a pivotal role in the story, or so people say.
Shun is eventually slated to die after confessing his feelings to Saki. Can't really say I'll miss him though, tough break.
Maria and Mamoru also have sex, and they are also going to die. There are some spoilers about them escaping after being condemned to death and then dying anyway but I am not clear on the specifics.
Saki and Satoru are the end couple, they eventually get married. Satoru makes the first move and they end up having sex at some point (not the tame stuff of episode 5, but then right now they are not really at an appropriate age for a sex scene from our point of view). And yes, that makes them the only survivors from the main cast. After their interactions in episode 5 I am somehow comfortable with that notion though.
Story wise, the material will progressively become darker and more complicated. From what I understand, the conflicts with/around the bakenezumi will continue to play a central role in the future arcs as well.