This is pure speculation, but what if the Doctor is being hunted by the Silence not for crimes that he has done, but for all those times he’s failed to intervene in mass crimes against the inhabitants of planets all through the universe? “Let’s Kill Hitler” revealed a lot, particularly about the nature of the Silents and the indoctrination of Melody Pond.
The Silents, it’s now clear, are a religious movement who will fall when the first question from the beginning is asked and an answer is given. We don't know what that question is, I but suspect the Doctor inevitably will provide the answer, and the question itself will have been hidden in plain sight from the start of this current series. We also know that the Silents grabbed Amy so that they could steal Melody,and Melody has regenerative powers from being a child of the TARDIS. The plan was to make her a weapon to kill the Doctor, although the motive for the assassination has not been stated beyond that the Doctor is a 'war criminal.'
But, perhaps “Let’s Kill Hitler” gives us a clue. We’ve been led to believe, in AGMGTW, that the Doctor is targeted for death because he’s a war criminal, but maybe we being misdirected as to what the Silence means by that. It's interesting that young Mels insists that mass deaths happened during history because the Doctor didn't intervene. Later, her careless “Let’s kill Hitler” also points to someone who wants or has been brainwashed to redress wrong, perhaps someone who has been raised to be like the Tessarects on a much larger scale, an avenger with the TARDIS the Silents grew who combs time and space righting wrongs, a savior who must first get rid of a false savior, i.e. the Doctor.
But, River/Mels finds herself confused when the dying Doctor crawls to the TARDIS in an attempt to save Amy and Rory. While she appears unaffected by her parents’imminent deaths, she is moved that the Doctor cares so deeply about them, and so she begins to change. In series 5, it’s no accident that the Doctor lands in Amy’s garden, nor is it an accident that Mels finds her way to her parents’ village, makes friends with her mother and learns about the Doctor through her, hoping that she will eventually lead her to him, which she does. As we know, TARDIS takes the Doctor where he needs to go, which was Amy’s garden, but she also keeps him from coming back for 12 years: just long enough for the friendship between Amelia and Mels to take root, making this timeline appear to be part of a plan.
There is also a religious/mythical overlay to the Doctor/Amelia story, which may very well tie back to the Silents and their religious movement. We have the Doctor asking for an apple from Amelia, alone in her garden while a serpent-like monster lurks within her house. Perhaps the Doctor is meant to be the godlike figure who walks with the Eve-like Amelia in her garden, but this god turns out to be a disappointment to the Silents who wanted a more hands-on brimstone type, and so they opt to destroy him.
And, then, there is the timey-wimeyness of the two series, missing years, missing months, missing days, lost time. The Ponds meet up with the Doctor three months after he leaves them on Demon’s Run. Presumably River’s gotten them home safely and then split, but where was the Doctor, and why’s he wearing the green coat. Why does he reappear wearing his tux, and where was he? And, for that matter, River’s dress when she meets the Doctor after the wedding is very 1930ish, like something she picked up at the Nazi banquet. Add to that, the Doctor’s visit to the Flesh factory, and there is a good chance there are two Doctors in the last two series: one the original and one a ganger.
Finally, there is this: the Tessarect captain says the Doctor must die on that beach in 2011 because his death is a fixed point, but the robot's navigator corrects him, saying “But time can be rewritten – remember Kennedy?” In our timeline, Kennedy was assassinated but in another, it looks like he wasn’t, and it’s looking like the Doctor’s death isn’t so much a fixed point in time, either, if this is an alternate universe like the one in CotBS. Oh, and while I'm at it, the Tessarects also grab people at the end of their timeline to give them hell, so why is River being taken now, when we know she will die in the future? This is not the end of her timeline Sounds more and more like two Doctors, and/or two universes.
ETA: I apologize for the hamfistedness of this essay. I wanted to get it down before I forgot my salient points. :)