It's interesting that the last few times they've met, the Daleks have coming looking for the Doctor. They've actively sought him out, for things like validation or salvation or to be cleansed of madness, and all sorts of other stuff they used to go to Davros for. This is because, in Nu-Who, The Doctor is God....
I don't mean a kind of ancient, pagan-style, hyper-exaggerated human being- someone faster and cleverer, with an uncanny knack for second-guessing his opponents, like Loki or Hercules. Loads of protagonists are of that type. Batman and Sherlock Holmes have those sort of semi-divine traits, as, of course, does the Doctor.
I mean in a more abstract monotheistic sense: Everything in the Whoniverse is oriented to the Doctor. All act for or against The Doctor. The Doctor is the contour map over which the energies of the universe ebb and flow. In the terminology of the show, he is the fixed point about which all else revolves and all is anchored and defined in relation to the Doctor.
It'd be nice to find a set of baddies just quietly getting on with something bad, without reference to the Doctor. The Ood had barely met the guy and they were singing his song and muttering prophecies about him. The Angels were pleasingly inscrutable at first, but now seem happy to pile into whatever end of season tag-team finale the other baddies have organised. The Great Intelligence seems incapable of directing his profound intellect beyond the activities of a single Timelord. The Cybercontroller wants to BE the Doctor.
We can forgive the Master - it's some familial Freudian Lacanian mirror type thing...everyone needs one archenemy, where it's all really about them,... but The Silence?... Have they ever exhibited any trajectory or motivation beyond a preoccupation with the death and the 'true name' of the Doctor? (The discovery of a hidden esoteric name... it's all very Dan Brown)
This is a consequence of the ramping up of the stakes.... when the whole of the universe is in peril, the Doctor must assume, by definition, a universal significance....though sometimes it'd be nice if, like Donna, we could all somehow magically forget that this were the case.