People have complained all this season that the arc wasn't as strong as previous seasons. There's a certain truth to that, but I think the difference is actually just that the arc wasn't as obvious
The "crack in time" and "who is River" arcs were very in-your-face, whereas the arc this season has been much subtler, constructed not out of plot hints and twists, but out of repeated themes and concepts and motifs.
Which, actually, is exactly how RTD used to do it.
Really, the solution to the Impossible Girl problem was basically Bad Wolf mark II. The only difference is that Eleven was aware of the arc's existence while Nine wasn't.
The first idea we were introduced to back in "Asylum of the Daleks" was that in the wake of last season, the Doctor had gone around removing himself from the history books. He left it so that no-one knew who he was. That was brought up again in "Dinosaurs" and "Angels." What does the GI do in "Name"? He goes to remove the Doctor from the history books, just taking it a step further by deleting all the good things he did, not just his name.
The Doctor visiting his own grave was a big plot point in "Name"... just as it was when Amy and Rory visited their own grave in "Angels," and present-Clara did at the end of "The Snowman." Clara got freaked out in "Hide" at the thought that her own dead body was buried somewhere in the Earth when the Doctor took her through her planet's lifetime. The Doctor himself does the same in "Name."
The leaf was introduced in "Akhaten" as the embodiment of all of Clara's life potential. It was powerful enough to subdue a god. Now we know why - it contained all of the Doctor's timeline and infinite lives, and was used at the end of "Name" to give Clara her identity back.
Echoes and reflections have been a consistent motif. The GI created digital echoes of people in "Bells." The time-travelling woman had been echoing through all of Earth's history in "Hide," connected to one particular person. The Doctor fights a reflection of himself in "Silver." The Tardis threw up echoes of itself to protect itself in "Journey." And of course the biggest echo of all - Clara, echoing all through the Doctor's timeline. Living and dying, living and dying... just like the Doctor.
There were constant references to previous Doctors throughout the season, especially the second half. He mentions earlier Dalek encounters in "Asylum." The GI itself in "Snowmen" and "Bells" is a Second Doctor villain. He mentions a granddaughter in "Akhaten" - a First Doctor reference. Ice Warriors are a Third Doctor villain, and "Hide" was basically a Third Doctor story. "Journey" contains soundbites and old props from previous Doctors. The 'gobby Australian' namecheck in "Crimson" is a Fifth Doctor reference. The Cyber-Planner-Doctor in "Silver" repeats Nine's and Ten's catchphrases. All of this reminding us of previous Doctors was obviously there to set us up for the revelation of a hidden Doctor no-one knows about here in "Name."
All of these things come together in the season finale, just much more subtly than the obvious "who is Clara" question.