I apologize for the lateness, and shortness, of this post. It's proving to be an interesting week and the buffer I had once had for the blog is long since gone. Will need to get that back up soon I think.
Anyhow, you can barely throw a stone in the direction of a Super Hero game of some sort without somebody wanting to be a villain. While the number of people that do want to be villains - at least the majority of the time - is fairly low in comparison they are still a good amount of the various fanbases. And why shouldn't they be? A hero is only as good as his or her villains and in many cases the villain is just a lot more interesting.
Don't believe me? Look at two of the most iconic heroes ever: Batman and Superman. Both characters are actually very boring on their own. Yes they are iconic, yes they define the genre, but as characters they are kind of meh. However, when you start throwing in villains like Joker, Lex Luthor, Lobo, Harley Quinn, and so on down the line the stories get very interesting. Because of this it stands to reason that there are some players who identify with the villain more than the hero.
Back to the table top, what do you need for a game with PC villains? Well, you need two big things. First, you need to have a long conversation with the group about what is and isn't allowed at the table as a meta rule. Some villains are very dark - even if it isn't explored how dark they are on panel/in show - and some players may be thinking that recreating some of that darkness is where the fun will be. At the same time, another player may not be comfortable with that level of bleak and evil being the main highlight of the game. So moreso than with any other game you need to have everyone on the same page as to what rating the game is going for and what is and isn't allowed. As the GM one of your chief responsibilities will be enforcing this rule.
The second thing you need is why it is so important for the ratings to be set in stone. You need pro-active players. Villains are the instigators of the majority of their stories, and so if the players want to be villains they need to be the one launching the adventures. Robbing banks, capturing the city, devising obscure and bizarre traps that may or may not be easily escapable. Those are all now up to the players. Now sure, sometimes the world can make the villains react. Many good stories involve the villains being "attacked" and having to react like their heroic counterparts often do, but for the most part the villains need to run the show.
There are a few other things that may, or may not, need to come up (hint: Super Villains rarely actually win in the end...) but those are secondary, or even tertiary, to the big two above. With those two you should be able to start. The rest depends on what you are going for rating wise, and what you actually want out of the game.