Sadly, I can't take credit for this essay - all credit to go to the brilliant Sohei over at the TGITF thread at Televison Without Pity. (Warning - several people in this thread utterly despised this episode, and they feel compelled to inform the world of this fact. At length. Repeatedly. The batshit is strong in that thread, which is a pity, when it contains genius such as this little essay.)
But in any case...
I find it best to think of it in mythic terms - whenever we see the Time Lords, on screen or in print, they automatically do the worst thing that you can possibly do to the Doctor - they treat him like he doesn't matter. The old series stories set on Gallifrey almost all have a Time Lord dissing the TARDIS as being antiquated and long past it's sell-for-scrap date. Chapter Cardinals talk to the Doctor as though his entire life, the way he lives, travels and gives his lives for what's right, is just a teenage phase. Lungbarrow is a painful book for me to read, because his Cousins, the spiteful, bitter crew of them, make him *small*.
The final scene of the Second Doctor is heartbreaking. He's gone through all that, only for his people to catch him. And punish him for daring to be a hero when they're not.
He's like the God that gets stamped down by the other gods for dreaming. And after he escapes, he's like Loki, or Coyote. or even Lucifer. This is a being from an unimaginably static, ancient civilisation based entirely on observation, secrecy from the rest of the universe and heartless destruction of anyone that might look like they might threaten them, and he's turned into the complete opposite. The Oncoming Storm.
And that, returning to topic, is why I loved this episode, and why I think it fits perfectly into the arc that's going on.
Rose treats him like a man with odd anatomy. She speaks in terms of dates, calls him her designated driver. When his alienness is pointed out to her she freaks, like with his regeneration ("you forget that he's not.. human"), his hand that still gives her the creeps, the way that he serially abandons his companions, or never visits when they leave.
But as with the way the Ninth Doctor completely changes demeanour when she's not around (especially in End of the World), when Ten is being all cockney and chummy it's his social facade. The Doctor as Rose seems to think of him - like a human boyfriend - is no more real than the drunk act he puts on in this episode.
Reinette is coming from the opposite direction. She thinks he's a lonely angel. She calls him Time Lord (has Rose ever?). She has to touch him to be certain he's flesh and blood. She reacts to him as though he's a magical being in the shape of a man.
And when he's with her, the act drops. Watch him, and watch him with Rose. With Reinette in that telepathy scene, the Doctor isn't putting on his human act.
He's not a man. He's a lonely god, a millenia-old wanderer in Time and Space. Until Rose gets that, their relationship can only be superficial. But with her coming to term with his regeneration, and with meeting Sarah in School Reunion, and lastly with seeing how he reacts to Reinette in Girl In The Fireplace, I think she's starting to get it. Where he's inhuman, and where he's anything but.
Which gives me tingly anticipation for the future episodes.
EDIT - I've thought about it some more. I've been detecting an increase in the show being couched in fantasy terms rather than science fiction ones - ever since The Parting Of The Ways, when the Emperor assigns him the role of the Devil. The Sycorax spoke of their technology as magic and accused the Doctor of witchcraft. The cat nun called him a Lonely God. There's the nature of Finch's offer to him in School Reunion and then this episode - seeing him almost like a fairy tale. He's being all myth-d up this year, isn't he?
Certainly something to think about.