An excellent way to avoid having a character with an overused personality is to avoid thinking of your characters as good or evil at all. Black and White is easy, that's why the world is painted in shades of grey.
Example: You want to tell a story about a baseball player's rise to fame, and you start with his childhood. Now, thinking in terms of black and white (or good and evil) the default picture to assume would be that this kid wants to grow up and become a famous baseball player. Now he needs a challenge, and a rival. The first thing to come to mind would, of course, be some bully who's trying to convince him he sucks at baseball and push him around. Not a terrible story, but let's try again in a couple shades of grey.
The boy is being taught to play baseball by his dad. He's not quite sure what he thinks of the idea, after all, those dancing shows were pretty awesome. But then when he pictures dad cheering for him up there in the stands, he gets this warm, fuzzy feeling in his stomach. So he decides he'll give it a try. First pitch he hits the ball out of bounds and a dog comes running up, grabs the ball, and darts off. This kid has to go chasing the dog down. He runs through the city park, wading through a stream and knocking over a couple picnic tables in the process. He comes out in the city and manages to corner it in a back alley. He wrestles with the dog, who's clearly having the time of its life, and manages to get the ball back.
Now we have a protagonist and antagonist who are already starting to build rich, interesting personalities without needing to be defined as good or evil. They're far from being black and white. In fact, just by throwing them in the scene together and getting the two introduced, we've already got them set up to encounter a myriad of realistic circumstances. Maybe they hear a gunshot or a mugging and get scared. The dog jumps up and stays by the boy's side, making sure he'll be alright. Now we've turned an antagonist into a protagonist with the snap of our fingers, and it was easy. Why? Because characters that aren't painted black or white are dynamic. They can switch sides at any time. Their motivations have no grounding in good or bad.
The dresden files in itself is actually an excellent example of this concept. Harry's foremost motivations are A: to employ his magic on a daily basis, because it's his passion and his main source of income, and B: to protect people, rather than hurt them. Marcone's primary motivation is control. Everything else is really just a means to an end, though Marcone's choice of means are rather unique in themselves. He earns money so that can create more companies. He creates more companies so he can exert greater control over a wider range of people. He "punishes" those who kill his employees so that he can operate his business without fluctuation. He does so because when he loses control of the situation, possible outcomes arise that he finds distasteful, such as the shooting of Helen's daughter. Often, Marcone finds himself in a situation where allying himself with Dresden is beneficial to his interests, since Dresden's goals would result in a more controlled environment involving one less adversary. Marcone is clearly and undoubtedly a bad guy. His criminal empire hurts people on a daily basis just to turn a dime, but rarely can he be seen as an antagonist to Dresden, which is why he's such a great character for Dresden to encounter. He's not particularly an antagonist, but he constantly maintains the potential to become one.
