Moffat has said he'll tie up some loose ends in the Christmas special. As for the silence. I thought we now knew why they were so concerned about Trenzalore? They knew if the Doctor went there then the Great Intelligence (or some other threat) could enter the Doctor's tomb and rewrite all of his victories. I figure their idea was to kill him early and prevent such a potentially devastating 'weapon' being left behind.
While that explanation does make sense, it doesn't really explain Madame Kovarian's attitude towards the Doctor or why she describes her conflict with him as an "endless, bitter war." Killing him to prevent a tragedy? Sure, I get that. But why do they treat him like a villain?
It's nothing we'll ever see, I'm sure, but I'd love to know more about the origin of the Silence. Where did they come from? How did they find out about Trenzalore in the first place?