Having just watched this video, in which an internet reviewer accuses Moffat of betraying the fanbase and emotional integrity of the characters whilst simultaneously undoing a whole series worth of development, I feel that I need to get my own thoughts out of my system.
I'm getting married tomorrow
Firstly, I'd like to recap the overall message of series five, as in many ways it pretty much tells us how six wil end. Five had the idea of fairy-tales and growing up. Amy spends her whole time running away from her wedding, travelling in the TARDIS as a way of escaping that responsibility and commitment. In the end she does both, and goes travelling in the TARDIS with her husband. She grows up whilst having childish fun adventures, and affirms that one does not need to exclude the other.
On her home planet, "Doctor" means "Warrior"
The overriding theme of series six seems to have been The Doctor's effect on the Universe, and the irresponsibility of his actions. This idea really first reared it's head during Smith's tenure when, in The Pandorica Opens, all of his greatest enemies descend on him. This is a direct subversion of one of Moffat's favourite tricks. Multiple times, The Doctor only needs to invoke his name to defeat his enemies, the very fear he induces being enough to tame them. As we hear in Forest of the Dead:
"You're in the largest library in the universe. Look me up."
The implication, of course, being that his name will be scattered throughout history, as well as records of all of his victories. He's using his long and actually fairly violent history self-knowingly, and that's bound to have an impact. In The Pandorica Opens, all of his enemies are able to team up against him as they believe he can destroy the universe. Fear of him drives them together, and when he, once again, invokes his name to scare them off, there is no small amount of irony. It's his history that has caused his enemies to get together at all.
This theme comes to it's climax in A Good Man Goes to War, when it's revealed that The Doctor is the target of the Silence's campaign.
"A war? Against Who?
Against you, Doctor."
The Order of the Silence, an organisation that calls think of themselves as the guardians of history, think they are at war with The Doctor. Between the army girl Lorna and River Song's speech, we are left with no doubt that this is an ongoing critique on the way that The Doctor travels and fights and destroys.
This is further hit home in the centre-piece of the secodn part of the series, with The Girl Who Waited and The God Complex. Both of these utterly brilliant episodes do incredibly interesting things with The Doctor. The God Complex couples him with the evil minotaur god that feasts on people's belief, suggesting he cultivates adoration from his companions and that he can only bring them harm. The Girl Who Waited plays an even more subtle and complex game, casting The Doctor as the villain in a tragedy that sees Rory have to let Amy die. Not only is The Doctor getting told he's doing the universe harm, but also his closest friends.
One of the best things about The Wedding of River Song is that it's rejection of such ideas. This may have been a series long deconstruction of The Doctor, but The Wedding of River Song is a reconstruction. His companions love him, and won't let him traipse off alone into that byronic hero suit that RTD was so keen on dressing Tennant in. Let's Kill Hitler hints at this, with the Tesselecta's obvious veneration of The Doctor, suggesting his death to be one of the worst events in history. If The Silence represents the negative legacy The Doctor leaves behind him, the Tesselecta shows that this view is not one shared by the rest of the universe. River Song shows him the signals that come through the stars, the replies to her distress call. The Doctor is loved, throughout the universe, and if he's had a negative impact he's made a stronger positive one.
He may have had a past that's been littered with conflicts, but he's also brought hope and made friends aplenty.
Even you cannot change this
The series starts with a prophecy: The Doctor will die by Lake Silencio. He has to die; we saw it happen. This is where series six both starts and ends, and much of The Doctor's fretting revolves around accepting his own mortality. The series is littered with things that must happen: River's already played out future, The Doctor's death, Melody's indoctrination. The Silence's ability to subconciously control people seems to suggest a certain element of people's future beyond their own control. In The Wedding of River Song, Amy and Rory get together again in a different time stream.
Much of the build-up, especially after Dorium's words, seems to point towards The Doctor accepting his own mortality. It's even suggested that it's for the good of the universe. So when The Doctor cheats this inescapable death, does that detract from all of his brooding over it, and attempts to come to terms with it? Funnily enough, River seems to have given us the answer already, all the way back in The Forest of the Dead:
"When you run with The Doctor, it feels like it'll never end. But however hard you try, you can't run forever. Everybody knows that everybody dies, and nobody knows it like The Doctor. But I do think that all of the skies of all the worlds might just turn dark if he ever, for one moment, accepts it."
"He just can't do it, can he? That man. That impossible man. He just can't give in."
The Doctor is not going to lie down and die. The Doctor will find a way, a third option, because he's The Doctor. He'll cheat time and history, and convince everyone he's dead if he has to. But that he finds a way out, rather than accepting that he has to die, is exactly what The Doctor would do. Or, at least, what Moffat's Doctor would do.
Series six's finale is, perhaps unsurprisingly, a subversion. It takes the ideas that had been proposed so far, the nuanced deconstructive work, and considers them, but ultimately turns into a celebration of the aspects of The Doctor that get lost in all the navel gazing. It's not undoing the work beforehand, but rather leading us to a different conclusion. It's not pulling new ideas out of it's ass, it's reminding us of how much more The Doctor is than all of that frowny stuff.
Series six was a messy affair, at times convoluted, and not as consistant as it should have been. A betrayal, however? No. It's not at the fanbase Moffat's sticking his middle finger at, but rather the idea that The Doctor has to be some kind of tragic, dark, lonely hero. He's taken The Doctor apart and put him back together again. Concluding the deconstruction with a celebration seems the only way to resolve it.