What about all of those "Great and Bountiful Human Empires?" Ignore everything the previous Doctors have said, why don't we?

The contradictions are dizzying if you think about them at all....

The Doctor could have reprogrammed them to their original functions, couldn't he have? So many problems...

And all those mind wipes... a new species, so he says, and he wipes their minds. It seems a big part of this series, I wonder if every episode is going to have a reference to it, and what's in that vault?