My favorite detail in this "alternative history" was that the whole transport system was hydrogen-powered! I don't think there was any explanation given; that world just happened to evolve that way. In teaching lessons from the text, I'd point out that alternative systems (transport, political, etc.) can always exist; it's whether we choose to establish them, or not.
A good topic to teach concerning any novel is how successful is it as a work of literature? In other words, how memorable, compelling, and effective is its use of words, including its organization of words into plots, episodes and paragraphs and its use of words in creating effective characters? (I am deliberately leaving out its use of words to convey ideas, because ideas in fiction get plenty of attention, although the use of words in conveying those ideas tends not to receive as much attention.) This question of how and whether words are successfully used seems especially interesting when dealing with a graphic novel.
One topic to address is men's violence toward women. This is relevant in Eddie's attack upon Julie and again in the problem between Blake and the Vietnamese woman he knew. Depending on the age of your students, you can approach discussion in a more or less direct manner, with more or less detail.
The obvious place to start for me would be to focus on the genre of the graphic novel and its recent rise to prominence in contemporary literature. It would be great to compare this to another graphic novel, such as the excellent Maus, and discuss how this genre differs from comic books but also novels or plays. What is added or taken away by the use of such a genre?
As for issues contained within the graphic novel itself, I think man's role and our own standards is one very important theme, as the character of Rorshach shows. Just because something is going to happen, does that mean we should give in to it or should be fight against it?
Watchmen is first and foremost a work of fiction, and so can take as many liberties with history as it wants. That being said, the internal history of the story contains some interesting extrapolations based on what might have happened had a truly Omnipotent super being existed during the Vietnam War. Dr. Manhattan singlehandedly defeats the VietCong, even if he does not win a war of goodwill. America's victory allows Richard Nixon to remain in power. The slump of Ford and Carter never happens, and so presumably the Reagan era never occurs either.
Another topic is that of moral choice. The character Rorshach was created by Moore as a parody of Steve Ditkos's Mr. A, an Objectivist superhero, and is very extreme in his thinking. Rorshach refuses to compromise; he will not reason with his victims and has no qualms about killing those he believes to be morally inferior or ethically incorrect. In the end, he confronts his beliefs up to the point of death, and although he does not compromise, he shows at least some signs of remorse or understanding. His character is in some ways the most honest in the book; he does not change his opinions for anyone or anything.
I think that the most obvious place to start is to talk about the graphic novel/comic book as a genre. Students think they know about comics, but there important for them to critically think about all of the varied choices the author and illustrator have to make when constructing a novel this way. For example, they should learn about the "space" between the frames and what that "means." I would suggest looking at the book, Understanding Comics, by Scott McCloud.
To some degree, the choice of topics to analyze depends on the grade level you are teaching.
A good starting point would be to discuss the emerging discipline of counterfactuial history and the controversies concerning its use as a tool of historical analysis. While, on the one hand, you can make thye case that asking "What if X rather than Y had happened?" allows students to understand X more completely, it is also true that it may be better to focus on the fact that Y did happen and ask instead why it did.
Counterfactual history also is a good entry point into discussion of the genre of speculative fiction as a form of social critique (or problems solving.)
Finally, this work lends itself to a cultural studies approach to popular culture. You might analyze how the forces of commericial necessity affect artistic choices.