I agree with most of what you said here (particularly the "Hallelujah" point -- what was the director thinking there? I was cracking up), but I have to disagree about the ending. While I buy that the alien would have been too out of place, I also have trouble buying that the rest of the world would band together when the destruction was caused by Dr. Manhattan. It's such a big deal that "God exists, and he is an American." If he destroyed lots of cities around the world, and only one city in America, what reason would the USSR and the other superpowers have to believe that Dr. Manhattan did this alone, and not because he was told to by his American government? The fact that we didn't get to know any of the NYC civilians added to the problem -- there was little reason to care the New York had been flattened, and it had no more resonance than the points on a map depicting the destruction of the other cities.

The end also seemed a bit... sentimental? I always thought the point of the end was that Ozymandias' scheme couldn't really work -- that, yes, he achieved this for now, but that it couldn't possibly last. That petty grievances would start up again sooner rather than later, and the millions killed would still be dead. This ending seemed to take at face value that we'd have this perfect utopia, and that Laurie and Dan were going to live happily ever after. The whole tone felt wrong, and it left me disappointed.

The first two hours were pure brilliance (especially the opening credits sequence!), but I think it went off the rails at the end.