Matt Smith quits as the Doctor
Matt Smith's Doctor said of John Hirt's character "I said he was me, I didn't say he was the Doctor". "The Doctor" is a name he gave himself to describe the kind of person he would be. This other person apparently did evil things that go against that. So Matt Smith's character says John Hirt's character is a version of him but not one recognizable as "the Doctor".
A lot of us old time fans believe John Hurt is the Valyeard, introduced in the 1986 fourteen episode "Trial of a Time Lord". The Valeyard (Michael Jayston) was the prosecutor in the Doctor's (Colin Baker) trial. During the last 2 episodes the Master (Anthony Ainley) appears to reveal that the Valeyard is in fact the dark side of the Doctor somehow brought to life between the Doctor's last regenerations (at the time the limit was 12, giving the Doctor 13 lives). How this happened is never explained. The Valeyard had to have crossed the Doctor's time line in order to be at the sixth Doctor's trial before he himself actually came into existance. He wanted to steal the Doctor's regenerations (7-12) to be free of the Doctor's morality. He also tried to murder the Gallifreyan supreme court justices.
If John Hirt is the Valeyard he's not a normal regeneration but an aberration and doesn't count among the 12 regenerations (or whatever they change the limit to).
Oh I forgot, another interesting theory, is that it was John Hirt's "Doctor" who actually destroyed Gallifrey. The idea being that a good version of the Doctor couldn't have committed such an act of betrayal against his own people, even if it ended the Time War.
Presumably, we'll find out more about John Hirt's Doctor in the anniversary special.