Y'know what I realised? This is the Doctor that has the possibility of becoming the Valeyard when he regenerates. If Moffat really is using a lot from the Classic series, he should have the Valeyard show up a time or two during Twelve's run. Not necessarily to try and kill him, but to try to manipulate him down a darker road, have him make choices in how he deals with the bad guys that aren't as noble as usual. And therefore increase the chance of Twelve becoming The Valeyard.
And not necessarily when he's awake. Pop up in his dreams as The Dream Lord and just talk at him.
Now that would a lot of fun to watch...