The Name of the Doctor is a surprisingly enjoyable finale for the season, as long as it's watched with your Doctor Who glasses on. Forget plot continuity, forget what's come before (even in Moffat's own run as showrunner), forget the fact that we don't really know who this so-called Great Intelligence is and live in the moment, and it's fairly dramatic and good fun to watch.
And if you can't forget all that... well, it doesn't make any sense.
This episode set itself up as the resolution to two big mysteries: why Clara appears repeatedly through time, and what the Doctor's name is. The idea that Clara had to be "impossible" to be an interesting companion was kind of wearing (what happened to the Doctor taking a huge range of different, normal people with him, just because they impressed him?), and I'm not sure I've met ANYONE who wanted to know the Doctor's "real name," but the resolution to both "mysteries" actually turned into a pretty compelling episode.
Of course, if you've viewed this entire thing as one continuous mystery, from the exploding TARDIS and the cracks in time onwards, it doesn't hold together whatsoever. This time, quite understandably, the loss of the Doctor through time was pretty darn destructive to the world, as people disappeared or changed entirely, and whole planets and timelines vanished. In The Big Bang, the only apparent change was that the stars all went out... but that was two seasons ago, so we'll have to forget that. We'll have to ignore any niggling questions about why the Doctor didn't notice the brunette stalking him through time for 900 years before this season. And if you're still wanting answers for why the TARDIS was exploding, or were hoping that "Silence will fall when the question is asked" would make a reappearance here, then it's probably best to put them from your mind. It's not going to happen.
But despite all that, the resolution to the whole Doctor's name debacle was surprisingly satisfying. The episode ended up stating what a lot of fans have said from the beginning: his "real name" does not matter. All that matters is the name that he's chosen for himself, and what it represents. A slightly contradictory statement, perhaps, given how much hype has been placed on this question, but a good one, and one that seems to set up the 50th Anniversary special in an interesting way.
As for the idea that John Hurt is a missing Doctor, possibly the "real" ninth Doctor during the Time War... it's definitely got potential. A lot of potential. The Doctor may often be presented as this great protector of the universe, but he's also very flawed, and he can be something of a narrow-minded, blood-soaked genocidal maniac when he chooses to be. So the idea that there's a Doctor who took it so far that he cannot recognize that regeneration as part of himself, and the question of how much of that person remains in him now, is compelling. Here's hoping it pans out.
The other mystery, of course, was who exactly Clara is and why she's spread across time. Once again, Moffat goes for a slightly non-sensical timeloop as his explanation. The Doctor travels with Clara because she appears across time, and he wants to know who she is. Clara in turns appears across time because she travelled with the Doctor, and became his friend, and decided to save him. Perhaps one day we'll get a resolution to this sort of thing that isn't "timey wimey" and entirely Doctor-focussed. But that day is not today.
Still, Clara's decision is kind of wonderful. She makes a noble sacrifice, bravely and with full knowledge of what it meant, in order to save her friend and the universe along with it. The puzzle of Clara, the question that was supposedly the most compelling thing about her, was all because of her own actions, her own choices. It is, in the end, all about her. An especially satisfying and surprising answer, considering the fact that this episode opened with a big speech about how Clara's entire life is about saving the Doctor. The speech was annoying at the time, but for once, it was actually true. Clara herself -- the real, original Clara -- wasn't all about the Doctor. But all of the echoes through time exist because Clara herself decided to create them, so that she could fix this problem and save him.
Unfortunately, framing her action as "saving the Doctor" minimizes what she actually did. Companions have saved the Doctor in seasons past, but they've also saved the world, and both those points have been emphasized. Rose was determined to get back to the Doctor in The Parting of the Ways, and she did save him, but she also saved Earth from the Daleks. Martha vows she'll return to save the Doctor and her family from the Master, but she's also acknowledged as the savior of the whole damn world while she's doing it. And now, Clara saves the Doctor's existence, and in doing so, saves a lot of the Doctor's allies, and in general saves the universe. But she's only ever acknowledged as someone who's saving The Doctor. She is fractured into many parts, all of them dedicated to the Doctor, and that's the only part of her sacrifice we hear about.
But despite this, The Name of the Doctor managed to resolve Clara's mystery in a way that was not only "unoffensive" (my greatest impossible hope, or so I thought) but actually fairly rewarding and empowering. I'll admit it, Moffat. I'm pleasantly surprised.