Several years ago I read an article about why Darth Vader is such a beloved character and why he is one of the most popular characters ever invented, despite the fact that he is so evil.
It has something to do with the way the bad guys are portrayed in the movies, and I think this can cover the Joe-verse as well. The bad guys are characters, you get to know them. Heck, all six SW movies are about Darth Vader, so you get to see him go from annoying child to even more annoying young adult to bigggest bad ass in the galaxy. You develop a bit of sympathy and empathy for him. You can identify with him.
While you don't quite get to see CC or Destro's entire lives, you get to know them as a person, not just bad guys.
I just watched the movie "Taken." (For those of you who haven't seen, see it, very awesome) I could care less about those bad guys because all they were was bad guys. The story didn't follow them at all, just their brief scenes before Liam Neeson killed them.
Now one could argue that the bad guys in Taken aren't likable because they kidnapped Liam Neeson's daughter and tried to sell her into sex slavery, OK, that's a very scum bag thing to do, but Darth Vader BLEW UP AN ENTIRE PLANET! He Force choked several guys just for mistakes. But why do we like him and not the bad guys from Taken?
Because the story makes us care about him.
Another part of this article had to do with the fact that you look at groups of bad guys, ie Storm Troopers, Cobra Troopers, even Hell's Angels and cowboys from the old west.
Nobody messes with those guys.
Strom Troopers maybe lousey shots and have some pointless armour, but you don't really see people walking up to them and talkiing smack. Cobra Troopers are the same.
Most people don't really aspire to be criminals or bad guys, but most people want to go through life just doing their thing with nobody messing with them. They look at these guys and see that nobody messes with them and develope a bit of an idea in their head that these guys are simply just too bad ass to mess with. People want to be bad ass.
Granted plenty of folks look to, for example, the military in the same way. People usually don't brag about bing a soldier or air man or sailor, but they will tell people that they are a Ranger or SEAL or Marine: the elite, better trained guys. Just so they can try to convince others that they are too bad ass to messed with.
People will also look at groups like the Hell's Angels and outlaw cowboys as people who are out there living their lives like they want to, doing what they want to do and not conforming to the norm. Lots of people want that and have that bit of admiration for those who can do it. They may not like the criminal part of the Hell's Angels, but otherwise the life style may appeal to them.
There's also the psycological dynamic that people love. How did this innocent slave boy go from being annoying but good to being a heartless jerk who is willing to force his own kid to become evil?
How did this car saleman go from a good life to becoming a tyranical leader of a world wide terrorist organization?
I may be talking out my ass and didn't make a lot of sense, but that's my two pennies on this.

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The United States will conquer Terrorism with the help of God and a few Marines.

Some people, when trying to avoid thinking about those things that cause them pain, turn to drink, or perhaps food, or drugs... I turn not to any of those... I collect action figures, turning my mind to the hunt, so that I might find a mote of peace... Over the years, I've found that alcoholism is much more socially acceptable by far.