Keep on, as Main Cast:
Peter - I wouldn't put him back at S1, but the Empathy with all the powers is a really great way to explore the Heroes universe... he doesn't need to be the main protag and source of the Apocalypse for another second, though... drop that tired line. He can't be the dreamer anymore.
Noah - Since they've killed off the 12, he's the best link we have to the Universe as a whole. Use him for that.
Hiro - LOST does a great job with flashbacks and flashforwards, Hiro would be incredibly awesome at exploring these.
Elle - Because she's kinda awesome, even though her storylines have been weak as heck. Imagine her with a good story?
Claire- "The Cheerleader" is kinda the heart of the series. If you want to overhaul the show, you have to overhaul her. How about separating her from the rest of the cast for a while? Claire undergoing changes is the perfect metaphor for the show undergoing changes. And her being her own person, as opposed to a simple minded adolescent, is great fodder to make HRG more than "For my family"-man.
Keep as recurring Cast/Guest Stars:
Mohinder - Character assassination aside, Mohinder is the best qualified to explore the science of the show, as well as the spiritual aspects. Humble him and get him back in a lab and with narrator's microphone. Bring him around every other episode or so.
Sylar- is tired and needs a rest. Give him an arc later in the season after the writers have some time to sit down and think about what he's done.
Ando- If Hiro's going to stop being comic relief, that means is comic relief partner gets to take a break too.
Molly, Micah- I just like them. And they're great actors for their age. They deserve a good arc, even if they aren't season mains.
Knox and Daphne Despite having no depth, these are great characters as recurring roles.
EVERYONE else can be removed, and perhaps even should be, dramatically so. That includes storylineless Matt Parkman, Nathan Petrelli the resurrection man, and anyone played by Ali Larter. I think these characters are around primarily because their actors are beloved. The characters themselves are worthless at this point, there is nothing that they do that could not be done better and more efficiently by an existing or new character. If they're so popular, spin them off into their own show, instead of letting them drag down Heroes into a clusterfrack of mediocrity.