Story is the apple, plot is the arrow through it. Plot is a sequence of events as revealed to the reader, but story is all the stuff in and around that.
http://terribleminds.com/ramble/2013/09/17/25-things-you-should-know-about-worldbuilding/
I think Moffat is good at writing plot, but he doesn't know how to write a story. In military parlance, story is strategy and plot is tactics. There are very few people who are good at both. Usually, a person is good at one, and lousy with the other.
I think it's the other way around; Moffat has a good sense of story, but he's lousy at plot.

Moffat effective at emotion, but he's not effective at grounding the emotion solidly enough in the plot to earn getting there. Hence, Moffat's Doctor Who often feels like a series of scenes in search of a plot.
I also think Moffat's era as a whole would've been more effective had he adopted an American writer's room approach, where the overarching season plot and the individual episodes are broken to within an inch of their lives and then farmed out to the writers.