Season 3 as a whole was not a bad season...it was just the first half of season 3 (seix episodes actually) that got people all up in arms. ABC decided to break season 3 up into two halves: a 6 episode run in the fall and then the rest of the episodes at the start of the new year.
Those 6 episodes in the fall were dreadful. They introduced the completely unnecessary characters of Nikki and Paolo, dragged out the Jack/Kate/Sawyer being held by The Others stuff with a little too much emphasis on Kate and Sawyer's romantic relationship, and killed one of the more interesting characters on the show in Mr. Eko (which I know was the actor's decision to leave but it still sucked).
The show turned things around in the second half of the season though but those first 6 episodes had the show looking
Yeah, I read about ABC splitting that season up. But since I didn't have to wait week to week to watch the episodes and I'm a Sawyer/Kate shipper, I enjoyed the hell out of those 6 episodes.
But overall Season 3 of "Lost" was definitely better than Season 1 of "Heroes". I mean just compare the finales for them. That Heroes Season 1 finale was a disappointing failure. While the Lost Season 3 finale was Epic, emotional, surprising, and set up the next season beautifully.