Hmm. As far as AM I'd argue that Morrison turned it into something else--and part of his point in his last issue was that he tried to use Buddy to speak about his animal rights concerns but that, in the end, it just wasn't a sufficient framework to build that on, and in the end in some ways it became a metafiction--about those very limitations I mean. (and I'd also argue that Jamie Delano's AM, which stopped being a SH comic after his first issue, in some ways is a more overall solid work) WATCHMEN, too, is really about those limitations. I mean, its point is that the normal way of superheroics is about people who solve only so much but never really solve the real problem. (And what is truly great about WATCHMEN has more to do with its structural brilliance than its genre) Ozymandias himself says that his action makes theirs irrelevant, and he's right. The best superhero comics are generally thought to be so BECAUSE they point out the flaws inherent in the genre and its insufficiencies, whatever form that critique might take. Besides, I think people who think of WATCHMEN as being about superheroes, as such, and as mainly an examination of them, are kind of missing the point. They're really a MacGuffin and the most superficial level of a multilayered work.
ZOT is fun(and makes you wonder just what the hell happened to McCloud's comics sense--oh wait, died of theory), but I wouldn't call it "great" in the same way, just to pull a name from the air, a Kubrick film is great(and Kubrick is very much like Moore in that each of his films is very much genre--SF and war more often than any other--but does them in such a way as it makes others following him look a bit inadequate) So's NEXUS, but that's really SF(or I guess space opera), and SF in general long since proved its capability to say plenty about the world, far beyond what superheroes do--it's a pretty broad genre and sometimes only a nominal one. I name PKD as an example, who should be discussed alongside William Burroughs and it's only the genre label that separates them(increasingly less now). Or perhaps DUNE and the fact it's really just a way of talking about the imperialistic relationship between the West and the Middle East, particularly the events of the Suez Crisis if you're thinking of when it was written. Or even Margaret Atwood or PD James. They speak of real concerns writ large, and I would venture that the true test of the limitations of a genre is: you hand someone the book. Do you have to make excuses for it to get them to open it?
With superhero comics, you ALWAYS, even now, have to do that. "Well, it's got superheroes, but..."
I would also put this test as well. Take what you think is a "great" superhero comic. If you remove the superhero tropes, does it still hold up? Do you need to understand the history of the genre going in to get it?