No doubt Moffat has something clever lined up; hopefully it's just not too clever.
I know all the publicity and Confidential references The Scream, but to me the Silence (or is it Silents? They refer to one as "a Silent", so maybe strange_complex is right) do look like aliens from a 1950s or 60s sci-fi film or cartoon, so I like the idea of dropping them into a story set in the 1960s. I also rather enjoyed Stuart Milligan's supporting role as President Nixon, for all its genial unreality.
There are a lot of loose ends, and I wouldn't be surprised if we didn't see them all tied up in this season. Amy's pregnancy is obviously significant: the suggestion is that the child in the spacesuit is Amy's daughter - yet also she has regenerative capability. Why does River Song get returned to prison? Certainly Moffat is writing about relationships in a more grown-up way than RTD. And - I think it's interesting - the TARDIS doesn't look "too full" to me with Amy, Rory, River and Canton all aboard as companions - provided you can give them all something to do (but preferably without Murray Gold setting all of them to music). I have the feeling we haven't seen the last of the woman whose brief appearance was credited as "Eye Patch Lady", though I'm not sure why - it just seemed incongruous and not immediately related to the story, therefore it must be there for some deeper reason. And by the end of episode 13 (which of course isn't due until the autumn), I presume we will have an understanding of why the event at the start of episode 1 didn't happen.