Engine, in addition to the usual Hollywood wrist wringing (e.g. telegraphing major plot points rather than show the viewer the clues and letting him put it together, or avoiding open endedness or endings up for interpretations, which the watchmen definitely has a ton of and relies on), they've cut the pirate comic sidestory that's central to the plot and to giving the plot one more perspective to reflect off of, they said they've changed the ending (too gory? too un-PC?), and even the director is protesting the cuts being made to the film.
Nolan probably got freedom to push this second batman movie as far as he wanted because with the first one he showed he could successfuly pull off the darker, more adult rendering. Not only does the Watchmen director seem likely to stray from the original comic at least a little by his own personal style like the Transformers director did (tho Snyder said he's inspiring/basing himself on some short film which Alan Moore helped make, details in the Watchmen movie wikipedia article) as you can see in the trailer, but there's also some things that leave very little room for error and that I reckon they're going to screw up.... E.g. the watchmen characters aren't up to artistic license as books' characters are, or as comic characters such as Batman which have been done lots of different ways by different authors/artists. The comedian character is nowhere near buff enough in the movie even though it's an essential part of his personality, and personality, psychology, etc are one of the top few things that made it such a great story.
Details like that, on top of all the classic "traduttore traditore" false notes in book/comic>movie adaptations, and on top of that the general Hollywood risk aversion in making a really authentic movie if it risks being too rude and violent... I think the watchmen movie would have benefited from seeing this latest Dark Knight movie clear the way for another movie in the same line of uncompromising story and illustration...
I hope that's not too rambling a post, but at some point in quality of story telling and demonstrative art, it's as good and valuable to culture (and personaly) as any other major piece of art.. And the watchmen comics were that good. It ought to be done justice to. Looking at what they did to Vendetta.... It'd be a shame to pass up an opportunity to make a movie that doesn't take viewers for idiots and also kicks bellybutton visualy. It could be one of those movies you can watch and still find really great 10-20 years later. Like 2001, etc.