If ratings are strong, they won't let the 13 regenerations thing stop them from making more. Off the top of my head:
1. River could've given him more then we realize. He expects to die after his 13th life and he doesn't and sits up amazed "Well that shouldn't have happened"
2. The "507" lives is canon, so, no explanation bothered with
3. 13 Finds/Meets a Dues Ex Machina that gives him a new Cycle
4. Time Lord Society comes back long enough to give him a new Cycle
5. Maybe someone who's People he saves, somehow transfers Life force enough for more regenerations
6. He somehow absorbed life from The End of Time brief Time Lords return
The explanations can go on and on
7. The 13th Doctor's final story arc centers on his mortality. He moves through the stages of grief, and as he accepts it, the time comes - but an outsider/outside force intervenes and the great surprise is that the Doctor resists having his life extended.
In fact, if it was me, I may do all sorts of takes on the reasons behind the 12 regeneration limit - probably going in the direction that the biggest reason for it is simply that after that, the process gets more and more uncertain, with a Time Lord who continues ultimately getting dottier and dottier with each subsequent regeneration. Sure the 14th incarnation seems okay, but one or two more and he or she has turned into the ultimate Alzheimer's patient. There's no quality of life, so it's best to end it then. The Doctor knows this and decides the time has come, and when offered an extension, he rejects it - but in the end, it gets imposed on him, and the big question that will follow him from that point forward is how much of his mind will he lose as a result, and when, if at all.
I would also at some point have reintroduced the concept of the Matrix - perhaps the Doctor would have discovered that, yes, some Time Lords did survive the Time War, but as disembodied minds in a computer archive somewhere. In short, they hid themselves away in the Matrix (for convenience it'd turn out to be hidden well away in the TARDIS itself)...so part of his arc would be figuring out what to do with the TARDIS. He can't just let it die, because it contains the minds of the surviving Time Lords in the Matrix archive, and he plans to download his own mind there when the final end comes - and that's when the outside force steps in.