Well, that was quite a reveal at the end of "The Name of the Doctor" wasn't it? It was a nice way to introduce John Hurt's character to use the same way they introduced David Tennant and Matt Smith, just to emphasise that, yes, this is The Doctor.
Several fans have suggested that John Hurt's character is '8.5' rather than '12', that he was the one who ended The Great Time War. There are several problems with this:
1) The Great Time War radio episodes are part of the Doctor Who canon and Paul McGann (The Eighth Doctor) is in all of them;
2) The destruction of the Time Lords and the attempted destruction of The Daleks is a known event and therefore lacks the necessary power to shock the audience into believing totally in the threat posed this new incarnation;
3) All the post-GTW Doctors have borne the guilt for the actions of the dual-genocide that ended the war, so it doesn't match up with the theory that by telling themselves 'he wasn't The Doctor' the other incarnations have rejected responsibility for his actions;
4) Never forget that The Doctor is a time traveller: there is no reason why they cannot have him overlapping his own future and past (although doing so breaks the First Law of Time, as taught by the Priadorian Academy of Time Lords on Gallifrey). So, why can't Ten and Eleven team up to fight Twelve?
5) The multi-episode epic "Trial of a Time Lord" back in the days of the Sixth Doctor, revealed an evil future incarnation of The Doctor called The Valeyard. The Great Intelligence referred to him too, which suggests that, contrary to a popular fan theory, Eleven's attempt to erase his intergalactic notoriety did not prevent that reincarnation from happening.
So, here's my prediction: John Hurt is going to be the result of a conditional time-line that has led him to become a villain that Matt Smith's 11th Doctor, David Tennant's 10th Doctor, Donna and Clara have to confront. He is a future, final reincarnation of The Doctor. Previously, it has been confirmed that a Gallifreyan can only regenerate twelve times.
My theory: There is a possible timeline where the Doctor, sickened by all the evil in the universe and heartbroken by all the dead companions who had fallen at his side during his long journey, decides to finally end it all - to end all evil and end wickedness once and for all. Not simply to end evil... but to prevent evil and wickedness from ever existing in the universe. To achieve that end, he proposes to do the unthinkable, to become an evil in his own right of such an astounding magnitude that even the Daleks and Rassilon Himself fade into obscurity.
The horrible thing is that, in his own mind, what he is doing is a grim necessity - the only way he can protect the innocent of all possible (and impossible) universes from the acts of the evil. As he said: "What I did, I did without choice... In the name of sanity and peace." Or as River so rightly put it: "Demons run when a good man goes to war."
A prediction now: We have yet to see the crime for which River was imprisoned. I suspect that, at the end of this season, after Eleven and Clara have been fighting, unsuccessfully, to stop Twelve's despair-driven plots for many episodes, they will return to the graveyard planet of Trenzalore before it was a graveyard. Eleven will gather his allies and call in his debts as will Twelve. Then, the two versions of The Children of Time, both good and evil, will clash and, there, it will fall to River to kill the greatest man she has ever known: A good, honest, and almost impossibly tired old man who was desperate to finally end suffering once and for all but who has to die to stop him from inflicting on all creation a horror far, far worse than anything previously imagined.
We'll be left wondering: Was this the inevitable destiny of The Doctor? Or was it a conditional time-line that Clara may yet be able to avert? Time is a wibbly-wobbly ball of timey-wimey stuff, after all; it is possible to manipulate it and, after all, is she not the impossible girl who always saves the Doctor? What better way is there for her to climax her career than by saving his very soul?