As satisfying as the finale is--and I did find it deeply satisfying--there are a number of serious logic problems that continued to plague me after watching it.
For one thing, time is all happening at once (an exaggeration--the Earth does not seem to be overcrowded with billions upon billions of humans and pre-human hominids all existing simultaneously, for example) as a direct result of River Song changing the outcome of a fixed point in time, namely the Doctor's death. However, a fixed point in time was also altered in the episode "The Waters of Mars," and the same effect did not occur. In that episode, history changed because of the Doctor's tampering, and then had to be changed back in an act of self-sacrifice. All of time did not happen at once. Clocks did not all get stuck on the same minute for eternity, Churchill was not the Emperor of Rome, and pterodactyls didn't fly in the park. Breaking the rules of time was treated much more gravely and maturely than that.
Second--and this is a huge spoiler, so really, look away if you don't want to have a major surprise ruined--if the Doctor is in fact the Teselecta shape-changing robot-vehicle and not the real thing, why did it bother growing a beard in the bubble universe? I mean, I know it's a shape-changing robot and all, but why bother when it was specifically pointed out in the dialogue that no one but him was aging? Why did Steven Moffat even include that exchange in the script when it adds nothing and only makes the logic more complicated?
Lastly, and this is perhaps the biggest logic problem of all, if the Doctor has to die at Lake Silencio in order for time to return to normal, how is it he fakes his death with the Teselecta robot but time still returns to normal? Was the fixed point in time simply that he has to appear dead to his enemies, at least for a little while? It hardly seems as monumental a moment in time as his actual death would be, and I thought fixed points in time were supposed to be monumental occurrences. I suspect this may be answered with some technobabble next season, but still, it didn't quite make sense to me. Don't get me wrong, I think the way he gets out of it is brilliant, but it was set up to be something bigger than that. (I'm assuming only River could operate the space suit and that's why they put her in it. Otherwise, with the suit doing all the work itself, she wasn't necessary to the Silence's plan at all. Though why the Doctor lets her take the fall and go to jail for his faked death is beyond me.)
Another serious problem I had with the episode is more a narrative issue than a logic one. Namely, all the plot closure takes place in the bubble universe, which then ceases to have happened. The Silence, Madame Kovarian, they're all still out there, undefeated, which means there really wasn't any plot closure at all. Judging by the prophecy Dorium kept going on about--"On the fields of Trenzalore, at the fall of the eleventh, when no living creature may speak falsely or fail to give answer, a question will be asked....Silence must fall when the question is asked"--it sounds like Moffat plans for the Silence to be the antagonist throughout the Eleventh Doctor's entire run. Of course, it's possible I'm misinterpreting what "the fall of the eleventh" means.
Speaking of Dorium, this character who never made much of an impression on me before suddenly became one of the highlights of the finale. The whole head-in-a-box comedy routine was brilliant. (As a point of little interest to anyone, I'm sure, I played a little D&D with some friends a few years ago and since I couldn't think of any particular kind of character I wanted to play, I asked the DM if I could play a wisecracking head in a box. He said no. Devastated as I was, I'm very happy to see someone else get the chance to do so now.) Also brilliant were the "living" skulls residing in the same tomb as Dorium's head. That was some wonderful, creepy, gothic stuff, and I loved it. Not so wonderful was Gantok falling into the carnivorous skull pit, though. That was the worst-looking thing I've seen on TV since the green-screen boat scenes in Ringer.
Judging by that same prophecy Dorium mentioned--"The oldest question in the universe, hidden in plain sight: Doctor who?"--it seems that if season 6 was about unraveling the mystery that is River Song, season 7 will be about doing the same with the Doctor. I am both excited and filled with trepidation. I haven't been all that pleased with the direction Moffat has taken the show in so far, especially this season, and I hate to see any more mystery taken out of it than he already has. In the meantime, though, the Doctor gets to travel under the radar and have lots of sex with River between seasons.
And finally, a moment of silence for the Brigadier. What a wonderful scene in the episode that was, the Doctor learning of his old, constant friend's death and understanding in that moment how foolish and cowardly he is to try to delay his own fate. In my opinion it was a brilliant way to make use of the real-life passing of Nicholas Courtney this past February without being exploitative. It makes me wonder if and how they'll address Elisabeth Sladen's passing in April. I dread seeing it in some ways, but I'm sure they'll do it with just as much grace and respect.
You know, during that scene where the Doctor learns the Brigadier has died, even if only for a moment, I felt like the show once more reached the emotional height it used to have during the Davies years.