They'll never do this, so I feel no fear in letting the idea get out there:
I would love to see a character who is, in effect, John Carpenter's The Thing.
To give you a Heroes-universe explanation, a disease that ate a Sylar-like character. The Disease would feed on healthy tissue by splitting it's body... sort of the way Beetlejuice did with his face when asked, "Can you be scary?" The creature splits apart, surrounds the victim in tentacle-like intestines and organs and cocoons the victim, and then absorbs it... effectively the cannibal I thought Sylar was once.
And then slowly over the course of a few hours, the victim begins emerging as the older tissue dies away and is discarded, until the creature thinks it *is* the last victim.
That, to my mind, would be something scary enough to make Sylar run the other way. He couldn't kill without using a method that could possible kill himself (like burning or acid). And would give Sylar an excuse for another heroic turn.