Heroes was wrecked from the first episode of Season 2. It may have been internally wrecked before that, but as far as I'm concerned, it was when Season 2 started that it hit the fan for the viewers in the worst and seemingly irreparable way.

The creators and producers seem much more interested in cashing in on the popularity of the first season. Talks of spin-offs were in the air before season one ended.

Continuity is completely out the window and doesn't look like it will ever be aligned. The writers obviously don't watch the show themselves or they'd realise that they're writing new episodes that just don't connect with previous ones.
The characters have all been put out to pasture. I'm sure this is all down to the writing and direction, since I find it hard to believe the actors have suddenly become less capable of delivering lines and the appropriate emotions. Clearly any early established character bios/traits have been thrown out the window. Everyone is acting out of character. It's as bad as the X-Files at its worst where you'd swear the characters' minds had been wiped and replaced with some stranger's every episode. If not every episode, then at least every few or at the very least every season.

The Suresh character for instancehas exhibited 3 or 4 different and conflicting personalities since season 1. Unless they write off season 2 and 3 as a giant dream sequence or explain that he and some others are afflicted with multiple personality disorder, it just doesn't make sense. Worse that that, it's simply not enjoyable.

Apart from that, I hate the Sylar character. Maybe if someone else had been playing him it would be different, but Quinto's portrayal just makes me want to skip his scenes. I still think it's down to the writing and direction though.