I haven't watched all of Heroes. Let's get that out of the way right now. I've seen the first season, about 80% of the second, and the first half (or so) of the third. I stopped watching because the story grew too complicated and because my favourite characters were being written out of character. It ceased to be worth my time. (I chose to write instead.) I've seen enough of the show to talk about it, just not the whole run.
I enjoyed Heroes, especially the first season. I loved the way it was laid out like a comic book, with all the interconnecting threads and stories. I liked the X-Men-like nature of the show, with people freaking out over their powers and using them opportunistically, with the powers being somehow genetic, with everyone banding together by the end to stop a nuclear explosion. I liked the moral greyness and the sense of this being our world, with our problems, and the characters being real people. The writers did a great job of integrating superpowers into this universe. I can almost believe the Heroes world is our own.
A large part of what made the first season for me was how every member of the ensemble (or the powered members, anyway) was going through a different version of an origin story, including several characters who came into their powers already aware of comic books and fandom at large. I liked that a number of them weren't in it for the superheroism and the saving of the world, but were petty and selfish and occasionally confused. See: realism, greyness.
The show started delving into more of the world, and more politics, in later seasons. We find out more about the previous generation of 'heroes' and the Company they founded to protect/hide people with powers. We find out about a virus that can give people powers and how a strain of the virus could cause a pandemic. We meet some of the more psychopathic and dangerous people the Company's captured as everyone trying to a) escape from them or b) recapture them. Several of the characters begin to go dark or grey. One of them does so while desperately trying to find a way to induce powers in normal humans. It's compelling stuff, good television, all of that—for the most part.
Like any fan, I have my quibbles, my opinions on how the show should've gone, what the characters should've done and changed into. I had problems with the fact that time travel, in the form of geeky Hiro and tortured Peter, was used to further the plot, to give hints and threats and clues, in the later seasons as it was in the first. One season, it's cool. Two seasons or more, it feels like the writers have a formula. I feel cheated. The same goes for the "save the world" plot lines, which, while cool, was done in season two as well. And then season three almost went soap opera in a few of the story lines and had characters who seemed to be there more for "aww, that's sweet" moments and dramatic tension, then to have a bearing on the plot. Claire's birth mother, for instance, and Daphne, the reformed thief who falls in love with Matt.
I digress. I have a suspicion that Heroes would have been more interesting for me if I'd had a good grounding in comic book tropes. I'm betting the writers used, twisted, or flat out sent them up a lot of the time. But it was still a good show, still portrayed a wide range of people and motives and situations, still had interesting things to say about superpowers and what getting them can do to a person. It wasn't black and white. There was no Justice as an ideal. Nobody really went out of their way to make random acts of kindness or save random citizens except when they had a more selfish goal in mind. (It was kind of an all or nothing show. Either they save the whole world, or they don't save anyone.) Possibly I'd have liked to see more altruism, but I'm not sure the show would've suited it.
I think the popularity of Heroes came from the fact that it was the first live-action, people-get-powers show on a major network, and the fact that it came out around the time when people were looking for complex plots, shows with clues and mysteries to figure out, and season-long, even series-long plot arcs. I think its legacy is still a little up in the air. Other networks are doing the people-become-superheroes thing right now, with No Ordinary Family on ABC being initially billed as a new Heroes and The Cape borrowing the comic-book layout and references. I haven't seen enough of either to comment on the plot arcs, but my guess is The Cape has that as well, as will some of the shows that are currently in production. Heroes certainly cemented the idea of 'real people, real problems, now with superpowers!" versus the "he's a superhero, watch him go!" that tends to come out of comic book adaptations, and perhaps that's the legacy in the long run. We like our fantasy these days to have its feet on the ground.