I really don't think we're seeing a "forgotten" regeneration between 8-9 here like people have been assuming. I think the key here lies in the past, specifically 25 years ago in the 25th anniversary episode of the show, Silver Nemesis.
At the very end the villian touches upon some of the very same plot points we see here:
"Doctor Who? Have you never wondered where he came from? Who he is? ...I know your secrets. I shall tell them of Gallifrey. Tell them of the old time, the time of chaos."
Of course nothing came of that at the time, but I think we're finally going to see that pay off now for the 50th anniversary... I believe the character John Hurt is playing is actually a pre-Hartnell incarnation of the Timelord we know as The Doctor. He was probably some sort of space Hitler initially who changed his name to the Doctor, stole a TARDIS and ran in an attempt to remake himself.
Plus, think about it; This way the numbering stays intact. Matt Smith will technically still be the 11th "Doctor", only he will have had more incarnations that we never knew of prior to becoming the Doctor which I think is a good compromise. I HATED the idea of Smith actually being the 12th Doctor.