So, I saw "Watchmen". I think that it is important to get the obvious problem out of the way first.
The comic has had such a devoted fan-base for so long that any adaptation was going to get mixed reviews. It has been (ahem) borrowed from extensively by everything from "The Incredibles" to "Heroes". The comic is so influential that the audience has seen a lot of the gags and big plot twists elsewhere. What was shocking and fresh a couple decades ago is now pretty standard genre fare. There is very little the Zack Snyder could have done about that. The other thing that Snyder is not responsible for is the extent to which history has over-taken the book. The story that Alan Moore and Dave Gibbons created in the '80s was very prescient. For better and worse, a lot their ideas came to pass. Plug-in cars are barely a novelty and the idea that a horrific terrorist attack on New York City might produce a brief moment of global unity is now history.
These factors add up to make the plot of "Watchmen" feel a bit like a super-sized episode of "Cold Case". This is hardly the end of the world, but it does make all the people who said that it was unadaptable (or required a 12-hour mini-series) seem a bit silly. David Hayter managed to get all the key plot points into a movie that ran less than three hours. It turns out that at least from a plot perspective, it is not nearly as dense as it seemed. However, the virtues of strict fidelity to the source material is often over-estimated by comic fans.
Good movies create a mood and draw their audience into it for a couple hours. While great movies encourage the audience to think about why they are feeling what they are feeling. Conversely, the inclusion of anything from that takes the audience out of that mood transforms a good movie into a bad one very quickly. This required the excision of a lot of meta-commentary by Moore and Gibbons about comics as a medium, but its loss is not very sharply felt. The plot and the characters work perfectly fine without it.
The more legitimate concern is that the loss of layers might adversely effect the core themes.
"Watchmen" is about power, in particular sexual and political power. Each of the central characters is defined either by power they have, power they lack, or both. Dr. Manhattan is nearly omnipotent, but he cannot control his personal relationships. Rorschach can pummel the faintly pathetic criminals of the piece into submission, but he lacks the political power that he craves. The Comedian has political influence, but lacks personal connections.
By and large, Moore gives his super people what they think they want. Often, the consequences are not what they expect, but they do tend to achieve their individual goals. However, Moore has surrounded them with normal people, who are largely powerless to effect their individual fates. There is the news stand guy and his nemesis. There is the prison psychiatrist and his wife. There is the lesbian cabbie. There are the two detectives. Each is sketched quickly, but memorably in the comic. Their fates matter to the reader and their powerlessness comments on the main action. Most of this content has been excised from the film to its detriment.
It is a shame, because status and power is a major theme in nearly every major work by Alan Moore. Yet, it never seems to make it into the Hollywood adaptations. "V for Vendetta" deals extensively with the psychological effects of being powerless in a totalitarian state. The plot of "From Hell" is driven by the relative power of the various characters within the Victorian class structure. Both "Swamp Thing" and "Miracleman" have characters whose perceptions change as their power relationships with the world around them shift. Snyder has no better feel for the power relationships that interest Moore than the Hughes Brothers or James McTeigue did.