Heroes is indeed a show that's been deeply, deeply flawed from the very beginning. I watched the first two seasons but for every thing I liked about it there were two or three things that annoyed me. Also it's very obvious the show has never had a game plan, and very much made up as it goes along. I remember when people were saying how much better Heroes was than Lost...something I've laughed at from the beginning. The only thing I can think of that made people say that (even though I don't understand why they could be compared, anyway) is because Heroes doesn't require you to pay as much attention.
The X-Files...I could also say this show's main problem was that it didn't seem to be as carefully planned out as it should've been, given the complex mythology. I didn't like Dogget too much but seasons eight and nine have some really good episodes so I don't regret them being made. Also, Scully was hotter than ever in those seasons.
I have only seen the first few seasons of One Tree Hill but it doesn't make sense it continue when you lose the two characters the show was mainly based around for its run...but then again people seem to still be enjoying it, and it's one of The CW's highest rated soaps so I could be wrong.