Apparently the gigantic telepathic squid at the end of Watchmen won't be present in the movie version. I would argue that it certainly creates a lot more work for the script writer; they have to make sure that this considerable change in the ending doesn't create huge, gaping plot holes in the rest of the film. The squid is such an integral part of the rest of Watchmen, with several scenes hinting at its presence until the dramatic reveal in the ending, that a replacement of it with something else would require dramatic rewriting of the rest of the novel, to the point where it might not even be a true adaptation, but just something inspired by the graphic novel.
On the other hand, you could certainly make the case that it's alright, as long as the ending keeps in line with the spirit of the book (i.e., a weapon of mass destruction being used on a major city to create the impression that the world is under attack by an extraterrrestrial intelligence to prevent all-out nuclear exchange). Which do you believe?