It's easy to forget how unforgivable some of the later developments were, but the first season of Heroes was utter brilliance. Coming at a time when then-King of TV Lost was going through a rough patch (unless you loved the meaning of tattoos), this ensemble drama about regular people suddenly gifted superpowers boasted some of the most tightly written plotting we'd seen on network TV. Tying together a myriad of plots together through its twenty-three episode run, culminating in a literally explosive finale, it quickly became a fan favourite.
The writers strike certainly affected the show in Season 2, with its storyline cut short and rushed plot points introduced that would take whole other seasons to right, but the real issue was series creator Tim Kring not having a game plan to deal with the incredible popularity. Although hints were dropped about where the story would go after the first run (feudal Japan, something about a virus), the general idea wasn't set and thus things began to seem sloppy. And when the fans registered their disappointment things only got worse.
The average second season was followed by a terrible third that bolted through convoluted plots in mere episodes, constantly trying to invoke the great early episodes (yet another exploding man, yet another trip to the future) without ever coming close to them in terms of quality.