1) Characters relate or don't relate on the whim of the player.
2) Hero has the Power skill for that. Otherwise, there's too much of "making up abilities as I go along". I'd rather have more definition to the abilities upfront.
3) Not all villains cheat. Some actually have their own code of ethics that they work by. Captain Mercenary won't do anything unless he has been paid in advance, unless it involves protecting his own hide.
4) Times have changed. The characters are really that powerful any more.
5) There is a flaw in your logic. Nowhere does there have to be parity between the heroes and the villains. Given your example and applying it to a game, if there is parity, then the Joker will always equal Batman. What happens when Batman happens to have Robin, Nightwing, Spoiler and Batgirl in tow? You now have your 250 point Joker taking a 1250 point beating, if all the heroes are also equal.
And lastly, some characters actual powers ramp up, becoming more effective, limitations falling off, etc. Most heroes, being loners, wouldn't be caught dead with followers and hate that they might have a fan club. After all, Mr. Incredible's arch-nemesis started off as "Incrediboy".