Spoilers below. Though, really, if you haven't read Watchmen yet, you're probably not going to and so they're not much in the way of spoilers.
As you've probably heard, they've gotten rid of the giant squid. That's understandable, since it was pretty goofy. However, in the new version Ozymandias makes it look like Dr. Manhattan blew up a bunch of cities to punish humanity for its warlike ways, providing the motivation people need to stop fighting and unite against their common enemy. This seems like an inferior substitute, especially since the movie makes pretty clear that a lot of the motivation is to get revenge—futile as it will probably be given Dr. Manhattan's power—against someone we know to be totally innocent if a bit naive.
One more thing: of all the Watchmen heroes, only Dr. Manhattan has actual powers, but he wasn't born with them; they were acquired in a science experiment gone wrong. With his name known (which it is in the Watchmen universe) it's pretty easy to work out what happened, so it's puzzling that nobody seems to have tried to repeat the experiment and make another Dr. Manhattan. Sure, it might not work, but it's reasonably likely that it would and given how cool those powers are, it's hard to believe you'd have much trouble finding volunteers.
Probably hard to make it through IRB.