This is somewhat inspired by the latest Issues with Heroes, though the problem is not exclusive to that show. In short, it really, really annoys me when there's not a proper Hero/Villain power balance in fictional works--be they movies, TV shows, books, etc. In other words, to have proper dramatic tension, heroes and villains have to fairly matched. When one of them is dramatically more powerful than the other, the whole exercise becomes silly and illogical.
In Heroes, the problem is that they've created a super-villain in Sylar who has an almost unlimited range of powers gained by killing other people with powers and stealing their abilities. For awhile, he had an evenly matched nemesis, Peter Petrelli, who could also absorb powers from other superheroes, and without the messy requirement of sawing off the tops of their heads. Alas, Peter lost his ability, and now Sylar is essentially unchallenged on the show in terms of superhuman ability. This is a problem. Not only does it mean that any limitations to Sylar's actions and choices are completely contrived (as there is no credible threat to his power), but it also denies us the possibility of a kick-ass fight between superheroes, which is quite a downer.
The imbalance can work both ways too. Take Superman, for example. Superman versus Lex Luthor has to be one of the dumbest match-ups in hero/villain history. After all, Superman is . . . well, Superman. And Lex Luthor is . . . really smart. I mean, that's all he has going for him other than a few bumbling henchman types. Not to mention that most of Luthor's schemes seem to revolve around real estate for some reason. Lex Luthor has yet to have an evil plan that couldn't have been foiled by a detachment of Navy SEALs. So why is Superman wasting his time fighting Luthor rather than rounding up terrorists or something?
I will concede that the drama can still work when one party is vastly more powerful than the other (generally the villain, since we all like the underdog), so long as the more powerful one has a giant, glaring weakness that can be exploited. That's the essence of bringing down super-powerful villains like Sauron or Voldemort, who dwarf the good guys in abilities, but can be brought down by a regular hero who understands that weakness. (And is willing to undergo some serious suckitude first.) Theoretically, Superman has the giant weakness of kryptonite susceptibility, but exposing Superman to kryptonite has become little more than a cheap stunt, so it's hard to take it seriously as a flaw. Not to mention that it's a logically goofy weakness. He's really super-powerful, except when he stands next to a rock from his home planet, which not only makes him vulnerable, but also appears to give him a hell of a stomachache. Fortunately for Superman, kryptonite is exceedingly rare--though Luthor appears to have a kryptonite tree in his backyard, considering how often he manages to scrounge some up for his schemes. You'd think that Superman would make some effort to rid the world of kryptonite in his down time, but every time he encounters Luthor with some kryptonite, it's a complete surprise to him. Maybe Superman's more glaring weakness is the lack of a short-term memory.