Hurts Doctor is...

An older version of Richard E Grants Doctor.
My theory goes as such:-

Richard E Grant was considered the 9th Doctor and it was his Doctor that fought in the Timewar. During the Timewar he did something uncharacteristic of the Doctor, like the mass genocide of both the Daleks and the Timelords, that he gave up the title of being the Doctor. To back this idea up you just have to look at the episode The Beast Below. "The Doctor: Three options. One, I let the Star Whale continue in unendurable agony for hundreds more years. Two, I kill everyone on this ship. Three, I murder a beautiful, innocent creature as painlessly as I can. And then I find a new name 'cause I won't be The Doctor anymore". So after the events of the Timewar he is no longer the Doctor, and therefore no longer the 9th Doctor.

Then some time passes and he regenerates into Eccelston. Being a new face and a new man he goes by the Doctor again, and because Richard E Grants Doctor gave up his rights to go by the name the Doctor, this makes Eccelston the new 9th Doctor. Richard E Grants Doctor is superseded from the Doctors memory.

This is also why Clara refers to Matt as the 11th Doctor. "You're the 11th Doctor!" To which Matt Smith replies, "I said he was me, I never said he was the Doctor". This would make Richard E Grant's Doctor an offical regeneration, and it would make Matt Smith the 12th regeneration.

So overall I believe John Hurt is playing an older version of Richard E Grants Doctor, who stopped calling himself the Doctor due to the events of the Timewar.

On a side note Moffatt has teased that people need to look at their DVD collections. This statement comes a week or so after Scream of the Shakla (Richard E Grants story) was released on DVD as part of the Doctor Who Classics. Including him that makes 12 Doctors available on DVD.