In particular, one train of thought is at once clear and yet also flawed. If the girl in the spacesuit in episode 1 is Melody, then yes, River Song "killed a Good Man" (hmm, a coincidental turn of phrase?). But it wouldn't seem to make sense that that is why she is imprisoned in another place and time; unless River Song is still following the plans of Madame Kovarian (surely, Servalan and Travis rolled into one). But then again, if the second half of the season reveals that the Doctor recovers the infant Melody, then The Impossible Astronaut timeline wouldn't have happened. I guess these are the sort of games Moffat likes to play.
So far, I've enjoyed this season; but apart from The Impossible Astronaut/The Day of the Moon and The Doctor's Wife, I do think episodes have often been riddled with holes (this is especially true of The Rebel Flesh / The Almost People). I wonder whether this is a retrospective attempt to weave a story arc into them, or if it's just uncharacteristic carelessness.