Season 6 just really felt like they said "Lets try and target our demographics." There was a lot less science, it was much more earth-centric, and the level of hand-waving was obscene.
The standalone episodes outshone the story arc episodes. Moffet seems to have realized this in planning for series 7. I for one am all for destroying the Doctor's magic wand, since it has become too powerful. A little more science and logic, and a lot less sci-fi and paradox magic would be nice.
