Season #1: Pretty riveting. There was just a lot of momentum and tension building up, Sylar was a ruthless prick, and there was very clear danger in centered around Peter's inability to control his powers. The plot convergence on Claire and the convergence in the cliffhanger finale were pretty awesome.
Season #2: Sucks blow through a straw. Like, what were they thinking? Aside from the problems with the writer's strike (that resulted in a very SHORT season), the plot threads were all over the place and there was little reward until late in the season. Ando back in time should have been shortened immensely, among other plot lines.
Villains arc: Finally, things start to pick up again. Nice twist in trying to "reform" Sylar, I thought Arthur Petrelli was a crappy actor, taking Peter's powers away seemed more of a writer's contrivance (what are we going to do, he's too powerful -- oh, let's take his powers, then give them back in limited form later!). Sylar deciding to go bad again at the end of the arc did make sense, and his relationship with elle was bittersweet.
Fugitives: Finally, we're back to something more resembling the first story arc way back in Season #1! Lots of action and interweaving of all the characters in the main plot. But we finally also start to get some complexity and newness between the characters, vs the stale relationships between a few pairs that kept repeating themselves. Sylar finally has moved on from his "kill 'em, collect 'em all!" mentality and started setting more challenging goals for himself; the whole mini-plot with him looking for his dad was very well-done, and the kid sidekick for a few episodes was well-written as well, with Sylar almost imparting fatherly wisdom to the boy and having this weird push/pull relationship, where it was believable that Sylar didn't kill him. I've got a few more episodes to go until the end, but right now Sylar has faked his own death and can now shapechange.
If I have any real griping to do about this series, it's that it still seems a bit more shallow than Lost in terms of characterization at times -- not nearly as bad as Once Upon a Time or Terra Nova, but basically characters come and go, the body count is damned high, and it makes it hard to care for any but a few of the main characters.... and even then, "lead characters" seem to die pretty regularly without warning, and the story just moves on. In a sense, this reflects the sentiments of mainstream comic books directed at the teenager population, but I wish there was more of a definite story arc in place and that the coming and going of characters had more meaning.
Also, while Fugitives has improved things, for a long time we were seeing some of the same interpersonal dramas playing out over and over, until I wanted to puke. I mean, if I had to deal with Noah and Claire's "daddy issues" one more time, I'll shoot both of them myself. Come on, girl -- the guy is definitely trying to help you, but he's toxic, just stay away from him!! At least mommy Bennett finally got a backbone and some complexity to her character, though, even if Lyle's just window-dressing.
Hiro and Ando are kind of cute together and comprise the positivity of the show -- Hiro doesn't get down easily, he brings levity and light-heartedness and the goodness of man to the show. Peter's the one with all heart that is a little more realistic in his analysis; yes, he's also an idealist, but he's not a fool either.
I despised Sylar for much of the series, until his reformative and then his resulting blacksliding. His character has become more complex, now that he's simply not just killing everyone he finds.