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Seemed to me like that intelligence enemy in the first episode will come back again. Does anyone miss the little things they used to do where an important name was strewn throughout the galaxy, Bad Wolf, Torchwood, 'the bees are vanishing'. Though I never found out what importance that last one had.
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I like the fact that under Moffat it has been more to do with a series' running plot, rather than simply vague hints being seeded in each episode. That was getting old.
The bees thing was to do with the Tandoka Scale and the migrant bees leaving Earth before it was stolen by the Daleks.
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.