!!!SPOILERS THROUGHOUT!!!
Just read IGN's review for Watchmen, and I think the guy had some pretty good insights.
He mentioned that the new ending passes by without really giving us a feel for the destruction, rather than seeing bodies in the streets, which a R rated movie could certainly do a lot with, we just see a few people get vaporized, which is something we have been seeing through the entire film. Where as in the graphic novel, we are really shown the gravity of what has taken place, and what a severe crime Veidt has commited.
Another thing the reviewer brought up was how, in his estimation, the new ending simply doesn't make much sense when you think about it. I thought a bit of this myself, but he really summed it up nicely. If you consider the fact that Dr. Manhattan was America's most powerful weapon that the rest of the world was afraid the US would use against them, and with the world being on the brink of nuclear war, if said US weapon were to suddenly be deployed and destroy several cities around the world, it would stand to reason that these other countries, rather than coming together in piece, would decide to strike back. It would almost be like us bombing a bunch of countries today with ICBMs and saying, "Oh my goodness! Our weapons attacked you with their own free will! We are so sorry, but you know what, they might do it again, let's ban together as one to fight this new common enemy that just so happens to be our very own weapons."
I still think the idea of a fake alien invasion worked a lot better. Everyone says it is very unrealistic, I suppose those readers somehow missed Dr. Manhattan during their read through of the series, he is certainly not the most realistic thing I have ever read in a comic book. With the faux alien invasion, we had the world come together to fight off an external and unknown foe. That makes sense, while these countries are bickering, some extraterrestrial force is out there plotting the destruction of the whole planet, why not come together to see what can be done to prevent this.
With Dr. Manhattan, everyone knows he is indestructible. Why even bother fighting against him, or trying to find a way to stop him? What good would coming together do? He'll win. That is why Adrian took so much care in getting him to go away prior to executing his plan.
I'd really like to hear from the perspective of someone who had never read the book prior to seeing the film. The film ending just had no real impact or emotion to it to me, when I first read the graphic novel there was a big "Whoa!!!" moment for me. I am really curious if people who knew nothing of the story came out of the theater with that "Whoa" feeling many people got from the book.