It’s important to recognize this in terms of gender balance. Since 1971, the “standard” model for Doctor Who has been a male Doctor and a female companion, and while this episode does explicitly note that it is possible to regenerate into a different gender, at this point in the show the Doctor remains a firmly male character, with female characters delegated to the “secondary” role. But The Doctor’s Wife consciously alters this, declaring that the series’ implicit hierarchy is in fact topped by a woman, and making female spaces a vital concept in the show’s mythology, in an entertainingly literal manner. And, because it’s worth saying, the fact that this is what the script emphasizes and not “spooky alien planet with a personality” can be credited to Moffat.
Really into Phil Sandifer’s recent Doctor Who posts, in which he teases out a feminist reading of the sixth season (The above is from this post, but the post about “Let’s Kill Hitler” is the central one in this argument, and one that’s sure to drive a bunch of people insane with fury).