After all, there is a precedent here. The Doctor’s Time Lord adversary the Master used up his entire allocation but was handed a new regenerative cycle after taking possession of a non-Time Lord body and later having it restructured (it's a long story).
However, Steven Moffat today confirmed of the Doctor, “He can only regenerate 12 times”, while simultaneously suggesting there has been a miscalculation of how many regenerations he has actually been through.
“I think you should go back to your DVDs and count correctly this time," said Moffat, "there’s something you’ve all missed.”
What can it all mean? If we were attempting to explain how the Doctor might already have had more than his fair share of regenerations, we could do it. John Hurt’s newly introduced dark Doctor would presumably add one, making Peter Capaldi the 13th and final incarnation. If we then followed the argument that David Tennant’s tenth Doctor used up a whole dose of regenerative energy when he re-grew his lost hand almost immediately after having transformed from the ninth Doctor, that would give us an illegal 14 versions of the Doctor. Whether the new hand counts as a full regeneration is very much up for debate, of course, but either way these are both arguments for adding not subtracting regenerations.
On the other hand (pardon the pun), we didn’t witness Paul McGann regenerating into either John Hurt’s ninth(?) Doctor or Christopher Eccleston’s ninth/tenth Doctor. If somehow neither of those counted as regenerations we would have one fewer than we'd previously thought – Matt Smith would be the tenth Doctor and Peter Capaldi would be the 11th. But how could the Doctor have changed bodies without regenerating?
Mofftroll strikes again. I am tired of this nonsense. Sorry if this is somewhat old news for you guys.