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It bugs me that the Silence plot was never actually resolved. The Silence creatures are still out there, probably all over Planet Earth. Madame Kovarian is still alive in this reality. And the Doctor isn't exactly being secretive about being alive any more.
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Sure, but pretty much every human will kill them on sight, so there's only so much they can do. I mean, unless they're broadcasting through mass media...
Besides, the Silence plot is very blatently not over. They're really playing up the whole "Doctor who?" first question thing, it's almost painful.
Clara is annoying, but not as annoying as I thought she'd be.