Here's a shakedown of my thoughts on Heroes after Season 3:
[sblock]Good:
Hiro depowered. I like Hiro's character, but his powers were playing havoc with any kind of believable storyline. If it was just teleporting and freezing time, that'd be okay. Time travel moves it from "powerful ability" to "you ALWAYS have to account for this in any plot." In any given situation, there was this dangling question; why doesn't Hiro just stop this? I dunno where they'll take him now, but at least the constant time traveling has ended. Arthur had it, but died. Peter had it, but lost it. Now the power's gone. Gone gone gone.
Syler evil again. As many have noted, Syler doesn't work as a dark hero. His moral quandry is okay as a sort of background element, but he works best as a villain, and this episode (indeed, this season) proves it. Indeed, in some ways he's even MORE of a villain now, since he's embraced that wholeheartedly and isn't just about stealing powers now. This could be good, IF they develop a good villainous agenda for him...searching out his parents won't last long, but could be good development. Sooner or later though, he needs to start diabolical schemes if he's really going to wear the Iron Mask of Doom.
Daphne. I like her. She's the sort of hero I'd play in a Heroes RPG.

She seems a bit young for Matt...but not scandalously so. They seem good for each other too, and it's NICE to have a relationship that's not tainted with hideous deception and betrayal and angst. I hope to see much more of them in Fugitives.
Nathan as bad guy. In season 1, we saw Nathan as someone who was willing to say the ends justify the means. That got lost in the hurlyburly in season 2, and I think season 3 sort of botched Nathan's twist from good to bad...but I think it's cool he finally got to where he is. This is a good place for him, dramawise. They need to develop him as this sort of sympathetic villain (contrasted with Syler's pure malevolence) in the vein of Magneto, perhaps. The bad guy you can't just kill.
Bad:
Angst Clair. It is my HOPE that Claire ends season 3 having matured and perhaps having lost her 'innocence' as far as people go...but not having become the 'harcore Claire' we saw in the various glimpses of the future. I can't buy hardcore Claire. Maybe it's not too much to ask of me...but I just can't square "badass soulless killer" with Hayden's adorable face. She does okay acting it...but even with slicked back hair and makeup, she is physically incapable of being intimidating.
Tracy/Nikki/Barbara. Admittedly, Barbara's an unknown quantity here, but frankly, none of these characters has ever really added anything to the plot of any season, IMO. It's not Ali's fault. The writers just keep including her even though her stories are essentially irrelevant and expendable. They need to either make her a -real participant- in the events, and not just an occasional throwaway presence...or stop using her.
The Uncertain:
Ando with powers. I'm not so sure this has the wreckage potential of time travel (I suspect not, but I may be surprised), but it concerns me for a couple of reasons. One, it means Hiro/Ando isn't being written out, most likely...which makes it increasingly likely Hiro will be repowered. Two, no cast thinning and another storyline to keep up with. Three, super-boosting other people's powers -does- have some breakage potential... Now, it has drama potential too (Syler kidnaps Ando to use him as a booster anyone?) and the idea of reversing the dynamic between Ando and Hiro...with Hiro now being Andi's normal sidekick...has some entertaining possibilities. For a little while. I just hope they don't obsess on it.
Peter with powers. It's been reset, it seems...which is good. He'll quickly regain his status as "the guy who can try to fight Syler," I expect...but someone has to be that guy. At least he won't be getting invisibility or time travel again. No Elle-Lightning either. Might work out. [/sblock]