It's interesting that Moffat's one episode to not be bound by the structures of the overall story arc for the series during the Smith era (well, the only one with his name on it) is this one. Rather than a structural timey-wimey piece like Blink or something that's generally regarded as pushing some sort of narrative boundaries within the series it's in (as with S1 and S4) we have this thing. Which is kind of weird in comparison, right?
It's almost like Moffat doing Davies, it's his most political Doctor Who episode in a lot of ways. Or, at least, it's his Doctor Who episode most about political institutions. Many of his others feature themes of feminism and social change, but not politics as an institution. Instead you have a searing indictment of the UK. It sees itself as an island that stands alone, adrift in space, cut off from everyone else. It functions only by oppressing an underclass (as it were) that people actively choose to ignore and forget about. Every five years people choose to forget what they know in order to perpetuate the system and continue to maintain it. All the while the undying, unyielding queen seems like a benign figure but actively participated in the original oppression of this underclass, even as she tries to forget.
And yet.... I get where Moffat is coming from in his comments on the show. I dunno. Maybe it's the refusal to go all the way - Liz X still comes off well in how she's portrayed even as she's not written sympathetically, technically. There are silly moments when I think there shouldn't be. It's juggling too much, what with being a companion's first outing and all.
You can see what Moffat was going for, and you can see all the good in the script, but at the same time you can see why he never attempted this again and was scared off. The solo episodes he did in later series that weren't plot related were Listen and (kinda) Extremis. And they're very different things. And I think it's a shame, because I don't think the flaw was the premise. It was just doing a little too much. I do hope he gets political (re:institutions) again in other shows, he so rarely does it.