If she is truly done with presidential politics, then a stint as vice president — in an office utterly bereft of power and full of hassle — is really not worth her time. She’d be better of retiring or continuing on as secretary of state (or some other post that has real power).
If she isn’t done with presidential politics, then it makes sense to leave the administration at the end of this term, get a campaign organized, and run either with or against Obama in 2016. That’s the real beauty of her situation at the moment: right now, she’s the only Democrat in the entire country who could be both pro-Obama or anti-Obama, depending on how the president is viewed in four years. If she joins up with Obama as the vice presidential nominee, then she spoils that.