I'd have some other ideas if the title weren't already "villains." And some of the ideas here are awesome, so I'll incorporate/build on them.
Main Characters (12 as usual): Peter, Matt, Sylar, HRG, Maya, Micah, Monica, Hiro, Claire, Mohinder, a new main character
As stated before, advance the storyline about a year (Cuz lets face it, it's going to be about a year before we see these guys), the Company has been refitted with two sets of partners HRG and Maya, Mohinder and Elle, and the season starts off with Mama Petrelli and Bob having a power struggle within the Company.
The Main issue of the season revolves around a new character, a Pastor Isaiah Rugless, who preaches that his god has given supernatural gifts to humanity and expects us to use them to change the world. He wins followers, even Gabriel Gray. Rugless who takes his own villainous name, and recruits other upset and discouraged souls with his message of empowerment and positive change. He "reforms" multiple would be villains (new characters that are "guest stars" like HRG and Sylar were first season or Bob and Elle were second season.)
Peter has spent the last year painting. First trying to find Caitlin (as he will explain later), only to realize he's sent her into limbo, then he sees World War III unfold around him in various paintings, and he doesn't stop painting until he has the whole story, a process that involves him spending the better part of a year filling a warehouse, or better, a "realigned" military base, full of paintings of this horrific war, this horrific future where superpowered people replace nuclear bombs as the controlling weapon, the one that the arms race is for. It turns out going public WOULD be a bad idea. He first goes to the Company, only to conflict directly with his mother, especially about Nathan, and then goes to get Claire's help.
Hiro in the meantime journeys to find others like himself, a mentor to teach him in the absence of his father and Takezo. He journeys to Ayers rock in Australia and meets an Aborigine young man who teaches him about the dreamtime, and, basically how real life mythos interact with the Heroes world, sending Hiro and a multi-point journey that gives him the answer to the war, while invisibly explaining how things are supposed to work, giving thoughtful viewers plenty to research and talk/think about.
Hiro's Journey finally brings him to Claire, who has been, by and large, living a normal life, albeit without her father. She cut a deal with Sylar to leave her and her family alone, and now Sylar can fly. (Evil, I know, and I liked West, but the idea is just soooo sweet I can't let it go).
Matt and Molly are partners as well, they travel the country, seeking out people with abilities and trying to help them. They live from check to check off of Matt's injury compensation. Matt uses his powers and skills and Mohinder's list to identify people, and Molly is used to actually find the people. About episode four or five they get into it tough and are saved by a vigilante duo of Monica and Micah when they are in New Orleans, perhaps even looking for Monica. They in their storyline, investigate Rugless's Movement and end up trying to bring it down, only to be conflicted, infight, and finally face off against the real villains united... Micah finally gets his 'fantastic four.'
Things get into focus by episode 6, all the pieces are in play and race towards the inevitable conclusion and conflict with the multiple simultaneous starting points for World War III. Cool episodes include "15 years later" where a grown up Molly, Micah and Villainous Kid are some of the last standing. This is where I would give a ginormous final battle between Sylar and Peter, SFX turned up as high as they will go. Sylar would win, and Future Peter would return, an old beat up man to the past to die at his own doorstep telling himself to paint or something.
But from episodes 6-end of the "half-season" conflicts between different characters just unfold rapidly with plenty of character development, background delving and relationship growth, culminating in a multi-front attempt to stop the world's biggest war, one that even the Company doesn't want.
On the emotional side: I would make Matt and Molly a bit of a comical VERY close father-daughter duo. I'd give Mohinder and Elle a bit of odd-couple style attraction going on. Maya and Sylar would be arch enemies, Peter and Hiro would develop a kind of 'we've been through a lot' friendship, Ando becomes big at Yamagato Industries, Molly and Micah would have some cool dialogue, and as for deaths: I'd have Sylar die saving Mohinder or Peter (after beating their behinds), I'd bury Claire alive in concrete (not in a coffin, but right in the concrete) until next season, obviously have the "Villains" turn on Pastor Rugless. Have Mama Petrelli double cross and kill Bob (or the other way around), and if I thought there was a cool way to lose Matt, I would say that, but I don't think that's necessary.
Just some thoughts.
