I actually hesitate to write this little analysis of the Doctor Who Series One two-parter, "The Empty Child/The Doctor Dances", because it's something that seems so obvious to me that I feel kind of condescending pointing it out. But everyone has their own little blind spots, and it's entirely possible that you could be a brilliant person with great critical analysis skills and insightful recognition of themes and still manage to miss the subtext of the story--which can be summed up with the sentence, "Doctor Who is the best show on television."
The two-parter is probably now best known for introducing Captain Jack Harkness, frequent Doctor Who companion and guest star and central cast member of the spin-off, "Torchwood". Captain Jack is a ladies' man (and a man's man as well), a swift-thinking con artist, a crack shot and a debonair man about town. In general, he's exactly the kind of character you'd expect to see go from a one-off guest star to a recurring character to a series lead. But the fact that this actually happened misses a key point--Moffat was taking the piss when he came up with him.
Essentially, Captain Jack is a "Hollywoodized" version of the Doctor himself, Moffat's vision of what the character would be like if all of the quirky, eccentric edges of the character were smoothed away by slick studio executives trying to make him more "marketable". Instead of being a "Doctor", he's a "Captain". Instead of being an almost-asexual alien, he's a sexy, suave human. Instead of having a time machine that looks like an antiquated British phone booth, he's got a sleek futuristic timeship (with a "cloaking device" instead of a "chameleon circuit".) He's even got a "sonic cannon"! He's everything you'd expect a sci-fi hero to be.
He's certainly everything Rose expects a sci-fi hero to be. in the first half of the story, he "scans for alien tech", he strides around boldly zapping things with his sonic cannon, and he charms her with his debonair, Captain Kirk-esque sexuality. Next to him, Christopher Eccleston's big-eared, big-nosed Doctor, who apparently looked at his screwdriver one night and decided it needed to be a little more "sonic", looks frumpy and goofy and generally not the kind of guy who gets his own series.
But in the second half, we see what the Doctor does that Jack doesn't (and what "Doctor Who" does that other sci-fi series only make a half-hearted pretense at.) He thinks. Underneath the scares (and this one has plenty), Moffat's been carefully concealing a fact about the Monster of the Week; it has a reason for everything it does. It's not just wandering around converting people into gas-mask zombies, it's following Nancy. "Are you my Mummy?" isn't just the catch-phrase of the week, it's the desperate question of a frightened child. The Doctor doesn't save the day with a well-timed punch or a zap from a ray gun, he saves it by figuring out what's going on and fixing it with kindness, compassion, and a heroic regard for human life. ("Everybody lives, Rose! Just this once, everybody lives!") While Jack, for all his swift-thinking con artistry, remains about six steps behind the Doctor the entire time. ("Like I said, I was there. Once. There's a banana grove there now. I like bananas.")
And in the end, when Jack makes his noble and heroic self-sacrifice, right out of the classic sci-fi mold, there's the Doctor, materializing on his sleek timeship with his clunky old TARDIS and saving the ostensible hero--and deflating his slightly-pompous death speech to boot. The Doctor, for all his "unsexiness", is the one who knows how to dance.