Four Types of Supervillains
Forget the ice claws, the glowing brains, and the hooks-for-feet for a minute. Despite their surface differences, all your supervillains fall into four categories: soldiers, menaces, masterminds and thieves.
The distinction is not about powers or how much of a threat they pose, it's about how the supervillain behaves. As a GM if you know a villain's type you know when you can best use him, her or it.
soldier — The soldier is the default supervillain: if a villain isn't clearly one of the other types, he's a soldier. The soldier commits crimes (or attempts other goals), fights when confronted, but tries to escape when necessary. When the heroes are knocked out, the soldier generally gloats and then leaves.*
menace — The menace is destructive. A soldier villain will fight, but generally tries to get away. On the other hand a menace villain sticks around and destroys things even when it serves no real purpose. The menace may not even like smashing things — misunderstood by society, it just might be how things turn out whenever he shows up (like the Neutron Fist, for example). Any encounter with a menace is a public threat. When the heroes are knocked out, the menace starts to destroy downtown.
mastermind — The mastermind is the schemer, the planner, the leader. The mastermind hatches the schemes that give all the soldier villains something to do. From the GM's point of view the mastermind is usually the instigator of all the interesting plots. If you check your list of masterminds and they are all in jail, it's time for a prison break. When the heroes are knocked out, the mastermind multitasks and puts the heroes in a cunning deathtrap while continuing the master plan.
thief — The thief doesn't want to fight, the thief just wants to take things and get out of there. You'd think that since supervillains are by definition criminals, lots of supervillains would fall in the thief category. Instead it's the reverse, with more soldiers than thieves. The reason is simple: if you want a superhero action game, who wants a villain who goes out of his way to avoid fighting? If the heroes are knocked out the thief escapes with the loot, but it's not likely to happen since the thief will try to get away rather than fight in the first place.
Again, it's all about the character's behavior, not abilities. Abilities just determine how successful or powerful a character is in the role. A mad inventor can be a genius but still act like a soldier villain type (resorting to direct confrontation instead of plots). An underworld thug might have nothing more than a crowbar and some streetwise, but still run operations like a mastermind. A phantom stealth character might still participate in combat like a soldier rather than avoid it like a thief. A massive brute monster might stick with the team and follow the plan, not rampage like a menace.
How common is each type? As a wild guess let's say most superhero games would have 70% soldiers, 15% menaces, 10% masterminds and 5% thieves. Change the ratios and you change the kind of adventures you get. If you have more menaces replacing some soldiers, you'll see a lot more mayhem threatening innocent bystanders. A higher percentage of masterminds vs soldiers means the mastermind has fewer supervillains to do the fighting, so expect more armies of clones/zombies/robots or “blow up the world” plots instead of masterminds leading teams of soldier villains.
These categories only address how a supervillain behaves, not why a supervillain behaves that way. Motivation and other subtleties of character are a whole different matter.
* Unless you're running a dark game where supervillains kill unconscious superheroes. Hey, whatever you're into.