Steven Moffat dropped some hints a few days ago about what was coming in the coming specials this year. First, he confirmed that the Doctor can only regenerate 12 times. But then he said, regarding the number of regenerations the Doctor's had:
"I think you should go back to your DVDs and count correctly this time...there’s something you’ve all missed.”
Dear Steven, trust me, I did not miss this:
I just assumed that you'd missed it. And no, I don't have any doubt whatsoever that this is what you're talking about.
I've always noticed this, I just assumed that the writers were choosing to ignore it. But when the Doctor was shot by a Dalek in "The Stolen Earth," he regenerated, but he siphoned all of his regeneration energy off into his hand, keeping him from regenerating completely. While this was exceedingly stupid writing, it should count towards his regeneration count.
So now we know that the 11th Doctor is actually the 13th Doctor. So that means that, as Moffat has confirmed that he will be following the 13 Doctors rule, something in either the 50th Anniversary Special or the Christmas Special will deal with the fact that the Doctor's out of regenerations.
So we deal with the Doctor's end of his regeneration cycle in the next few months.
But if the 11th Doctor is really the 13th, then where's the Valeyard? The GI said that the Doctor would be known as the Valeyard by the end, but if he really is the 13th Doctor, the Valeyard should have been created already.