We have always done the same kind of work. Our methods have not differed as much as you pretend. I am a shadowy reflection of you. But it would have taken only a nudge to make you the same as me, to push you out of the light.
-Indiana Jones and the Raiders of the Lost Ark (1981)
The hero won't be spending all his or her time at odds with other members of their supporting cast. Heroes need their villains because one side helps define the other. The best sort of hero/villain throw downs are those in which the villain, using his power, abilities, origin, personality, or some combination of the four, provides a direct contrast to the hero. He is the hero gone wrong, the hero who is sent off the deep end.
*Comics legend Peter David states that it's the same as the heroes and their arch-enemies. More often than not, they both work at the outer edges of the law. In the old days, the main way to tell the good guys from the bad guys was that the former would refrain from delivering the coup de grace. With the likes of the Punisher and Red Hood (Jason Todd), that line of demarcation has been erased. When the good guys throw punches with the bad guys, like as not, they're trying to put down their opposite numbers.
Recalling on internal conflict, the hero has to not only battle external forces but the darkness within himself. If man vs. himself is done properly, the villain in some measure, reflects aspects of the hero that the hero would rather not address. In working to defeat the enemy, the hero is battling his own darkest impulses.
A prime example of the contrast is Incredible Hulk: Future Imperfect which puts the Hulk in a literal battle against a future version of himself called the Maestro who ruled a distant future with an iron fist. Peter David and George Perez took readers on a psychological trip in the second half of the book when the Maestro tried to bring the Hulk over to his way of thinking. What made the conflict so daunting for the Hulk was that he knew the potential of becoming the Maestro was deep within him.
*David says not every villain needs to be an exact reflection of the hero. But he shouldn't be interchangeable with someone else's opponent, either. Both in terms of power and personality level, he should tie in thematically with the hero so that he is unique to the hero he opposes.
Take Mr. Fantastic and Doctor Doom for instance. Both are extraordinary scientific minds and explorers who seriously botched their endeavors which had taken different directions. Richards brought Ben Grimm, Susan Storm, and her brother Johnny on a space expedition that exposed them to cosmic rays thus spawning the Fantastic Four. However, Reed ignored Ben's cautions about sufficient shielding to keep the cosmic rays out of their craft. Victor Von Doom was conducting an experiment to communicate with a another dimension. But for his troubles, the experiment went sideways and it blew up, leaving him disfigured. Of all the twisted aspects of Doctor Doom is that he blames Richards for the miscalculations of his experiment.
In writing battles of good vs. evil, we should think how the villain is a contrast to the hero.
*Writing for Comics & Graphic Novels with Peter David pg. 86