The counter-argument has been that (a) that limitation may have been something imposed and enforced by the Time Lords themselves, and since they're no longer around, the Doctor has some flexibility, and (b) River's giving up of her regnerations may have given the Doctor some bonus lives. And, of course, (c) it's a TV show and it's Steven Moffat.
That said, it seems Moffat does accept the 12 regeneration cap. Which doesn't mean he doesn't have a clever way to get around it, but it should lead to further speculation about how that would work.
In other, possibly unrelated news, Moffat said he's "open" to a return of Jenny, a one-off kinda-sorta-clone of the Doctor from some seasons past (http://en.wikipedia.org/wiki/The_doctor%27s_daughter). And Peter Capaldi will likely use his native Scottish accent in as the Twelfth Doctor.
‘Doctor Who’s Steven Moffat acknowledges regeneration limit
Steven Moffat acknowledges The Doctor can only regenerate 12 times.
Woot!
Glad to hear that Moffat is keeping the canon straight in the Whoverse.
Master stole a body to get more.
Well, based on what has happened thus far it would appear that when the master stole Tremas of Traken’s body, he got another 12 regens since he regen’d on screen from Jakobi to Simm.