[Spoiler (click to open)]Clara is a delicious mystery. From what we're told, a perfectly ordinary girl, but also somebody who has died twice and still exists. Can we take her at face value, or not?
In "Hide," Emma told the Doctor she was perfectly ordinary. Let's suppose that is the case. (Well, ordinary except for having been uploaded into a virtual world run by the Great Intelligence, given an intelligence upgrade, and downloaded back into her body. I suppose that's as ordinary as you get in the Whoniverse.) Let's suppose that Clara was born of two ordinary human parents and grew up without anything supernatural happening to her, and whatever made her also exist and die in other times and places happens later. Okay, that's possible.
But then again, Emma told Clara not to trust the Doctor because he had a sliver of ice in his heart. If Emma doesn't trust the Doctor, can we trust what Emma told the Doctor?
In the teaser for "Journey to the Centre of the TARDIS," the Doctor asks Clara, "What are you? A trap or a trick?" That's entirely plausible. The episode where we first met Clara/Oswin began with an ordinary-seeming woman who was completely unaware that she was a Dalek trap.
If she is a trick or a trap, whose? The Great Intelligence springs to mind. I love that we have no idea what he is after. And with a name like the Great Intelligence, he is an enemy who would do battle with the Doctor with smarts as the tool. Who could possibly outsmart the Doctor? And how?
Psychological warfare. A battle of nerves. Induced paranoia. Over what? Over Clara.
You take a perfectly ordinary woman and drop hint after hint that she might be something other than ordinary, that she might be a trap or a trick, and little by little destroy the Doctor's trust in her, and (since he depends on his companions to keep him sane) in himself. That would be clever.