I tend to root for the underdog.
So when I see a plucky little hero, facing an army of hundreds guaranteed to cause massive amounts of damage much too soon to stop, led by a being of unimaginable power who has been planning every contingency for the last five years, I feel sorry for the guy. The super-villain, that is. Because is there any chance in hell that he's going to succeed?
Let's get the whole evil thing out of the way right at the beginning. Yes, the villain is vile. He is homicidal and greedy and if he got his way innocent people like yourself would be in big trouble. Nothing in his sob-story past can justify his actions. And general insanity is a diagnosis, not an excuse.
But does anyone deserve the life of a super-villain?
Think hard: Have you ever read a story involving a contented super-villain?
A villain may try a hundred different plans, each one more ingenious than the last. Not one of them is ever going to last for more than a few minutes once a hero gets involved. It's Wile E. Coyote and the Road Runner! And between plans, there are years of prison. So the man is caught in a loop, where he always knows that the closest he's ever going to get to happiness or meaning is the five minutes of anticipation where it looks like he's going to make it.
One side is always going to win, the other side is always going to lose. So it comes as no surprise that a lot of bad guys try to switch sides. It never sticks. Others have tried getting out of the game altogether. That never sticks either. Sooner or later, a super-villain is going to start acting like a super-villain again.
(I wonder why that is. It might be that, robbed of their climaxes so often, they become obsessed with the false hope of winning. If they can beat the hero just one time, maybe that'll make up for all the misery. Or maybe there really isn't any cause, and these people are just wired that way. Some of these characters are so completely devoid of humanity that it wouldn't even occur to them to do anything but crime.)
Whether or not he sees it, a super-villain has nothing to live for. He is never going to get to the top of the world. He is never going to beat his nemesis (though he may come tantalizingly close several times!). He is never going to destroy society, or get rich, or whatever other big plans he has. All he has is the loop. Get out of jail, build a comfortable empire, crescendo towards an actual achievement, see a hero, go back to jail.
Efforts to break the loop are doomed. The best of prisons is still a joke. Brainwashing of either side is guaranteed to wear off or be undone. If a villain leaves town, the hero will coincidentally happen to take a trip to wherever he is on the day of his big job. If the villain tries to stay off the radar, the hero will hunt him down. If the villain is banished to another planet or another dimension, he'll just come back angry. Anything less than death is not permanent enough.
So my first instinct is to yell at the heroes: "Kill him already!" For the sake of society, because the future and certain threat needs to be removed. For the sake of the hero, because if the job isn't finished he can't move on to other things. And for the sake of the villain himself, because what sort of life is he living? End the pain, already!
But wait. Death isn't permanent either. Once a super-villain has established himself, he's created a position in society that will never go away. The next time someone thinks they need this particular set of powers for a job, back out of the grave he comes. You know how it is. And even if he's lucky enough to stay dead, someone else will pop up out of nowhere to take the name (and the misery). And if that person dies, another one pops up. And again, and again, until the original villain is so annoyed by the copycats that he resurrects himself, just to stop involving other people!
There's only one way that a superhero story can have a happy ending. And that's if it doesn't. Let the bad guy win! Let Charlie Brown hit the football!
I want to see Doctor Octopus outsmart Spider-Man.
I want to see Magneto enslave the ordinary humans.
I want to see a season of 24 where Jack Bauer is killed and a big chunk of America is lost.
I want Marvel's new crossover Secret Invasion to end with the alien invaders taking over the world.
I want DC's new crossover Final Crisis, whose tagline is "Evil Wins.", to actually mean it in the end.
I want those annoyingly lucky heroes to get what's coming to them!