There's been something of an odd variety of stories over the years, Doctor Who's had the advantage of shows like Stargate: SG-1 where, if you make the regulars smaller, you have the premise to put them into such a wide variety of situations, Doctor Who even being able to change the entire cast and use all of spacetime as backdrop; stories like Full Circle sure had twists I didn't expect. Though, I don't think the rebooted Doctor Who's gained much at all from the series-long mysteries/arcs. I've liked a few of the new-era two-parters but, admittedly, also some one-parters like Blink.