So what could you take away from A Good Man Goes To War as a GM?
You can have a big finale (or something like one) with no real foreshadowing of major elements. A huge army and a villainous scheme dedicated to screwing up the Doctor's life, that we don't really know much of anything about. They're human, from some time in the future and... that's it really. They'll matter more later, presumably. But there they are, big as a finale, no buildup at all, we're dropped right into it like any MOTW.
Similarly, with a character as old and storied as the Doctor, you can indulge in gaps and this indulges in a lot of gaps, as long as there's some backstory. This basically introduces an entire superhero team of people we haven't actually seen before, with guest appearances from people we have.
They could be a model for a different sort of game, too, a group of powerful and weird beings united against a common foe. It could certainly work as a change-of-pace one-off.
Likewise, no matter how bonkers an idea is, the Whoniverse can support it. Victorian lesbian Silurian vigilante with a katana? Sure! And I was worried I was being a bit daft with Sea Devils sneaking around the docks...