One interesting issue when designing a superhero roleplaying game is how to handle the vast disparity in power levels between characters considered to be superheroes. If you allow the players to imitate any characters from the comics, how can you play a game in which Captain America might fight alongside Thor? If you try to model the game in a realistic fashion, the results would be bizarre. Any attack which can hurt Thor at all should kill Captain America instantly with any hit. And any opponent who can withstand even a single attack from Thor should be immune to Captain America's martial arts attacks.
When designing a superhero game, you need to have an approach to handling these issues. And the fact that the comic books are unrealistic in this way isn't necessarily bad or something that needs to be fixed; I myself like to model the classic comic books and intentionally recreate the unrealistic action in them. But this means understanding how the action seems to work and what your game will do to deal with issues relating to the great variation in the scale of attacks and defenses in the comic books.
How do traditional superhero roleplaying games handle this issue?
Compression of Scale: This is a classic in superhero games. I tend to think in particular of Champions. Characters can have vastly different power levels in terms of conception, but the game mechanics ensure that they can engage in combat with one another and still enjoy a good slugfest. When a high-offense character attacks a low-defense character, he does a lot of damage, but not an unlimited amount of damage. And a low-offense character can cause a small amount of damage to a high defense character. Typically interactions with the unliving world are also scaled, so that strengths can vary a thousand-fold and strong characters can bust through concrete walls while weaker ones have to make a roll to pull the door off of a car. This approach gives great freedom in designing and playing characters who act like the comics, while still making possible a well balanced combat system; it is my favorite approach. The disadvantage is that a lot of edge cases tend to feel odd and unrealistic. If you are really thinking of the game as a comic book, it can be hard to envision how the martial artist can be grabbed by molten lava man without ending up in the burn ward, or how he can get lucky and karate kick his way out of a prison cell. You need even more suspension of disbelief than you would in an actual comic book.
Fixed Character Power Level: This is another mechanism that can work very well in superhero games. The game may allow you to be many different types of superheroes, but all of these superheroes end up having a similar overall power level. The game does not try to mimic the vast disparities between the power levels of supers in the comics. This approach feels more realistic than Compression of Scale. Everyone can engage in bang-up battles just like the comic books, and everything feels just about right. The down side is that the characters can look like classic comic book characters, but they clearly can't quite be the same. You can make a character who looks and acts like Superman, but he can't really lift the space shuttle into orbit or survive howitzer shells without a scratch. You can make a character with the attitude and super-senses of Daredevil, but he is also a "meta" with steel-hard skin and super-strength, who can't really go on an adventure in which he faces an ordinary human crime lord and is overwhelmed by hordes of martial arts minions. But as long as you don't mind matching your conception to the setting of the game, everything works great.
Harsh Reality: Many games just don't really deal with the scale issue at all. You can make characters of greatly varying power levels, and those characters are not balanced at all against each other, so fights can be lopsided and brutal. By "not balanced at all", I mean that they may be equally good overall, but they are not balanced so that a slugfest can really work. Maybe one guy controls minds, while the other is strong enough to kill with one blow, so the fight is decided by who can attack first. Such a game can work, but only if it is understood that the game is not trying to model a classic comic book reality, but something quite different. Typically this works well with games that are attempting a modern rethinking approach to superheroes - "what would happen if people had superpowers in real life?" I think of Aberrant as an example of this. The harsh reality approach is really meant for a game that encourages a "combat is rare and very scary" approach, with a focus on storytelling and noncombat activities. I am generally rather disappointed with games that use the harsh reality approach, but pretend to be a 4-color comic book game when you design the characters. You can make your classic comic book character, but once you start playing, you find your character had better change his entire outlook on life, lest he end up dead or booked for manslaughter. Unless the GM simply mandates that all characters have reasonably comparable attacks and defenses, in which case the game is transformed into Fixed Power Level.
How do the comic books handle these issues?
Compression of Scale. Often, in the classic comic books, big attacks are more powerful than small attacks, but not as much more powerful as you might expect. For instance, a superhero who can lift 50 tons may fight a supervillain who can lift 10 tons. The supervillain may appear to be outclassed, but not nearly as outclassed as you might logically expect when one guy is 5 times as strong as the other. Compression of Scale is often used when, visually, you can get away with it. I remember several times in the Avengers when a mighty villain would make his entrance with an explosion that flattened all of the Avengers. It looks good in the comics. But realistically, one explosion is not going to have an equal effect on Avengers of vastly different toughness levels.
Rationalization. Many comic books characters will give excuses for why attacks between vastly mismatched opponents can have the effects they do. For instance, a character with low defenses will say, "Good thing that attack only grazed me, or I'd have been killed!" Good thing the attacks always just cause grazing hits! Or a villain will grab him and say, "I'll crush you like an overripe melon." Odd that the panel makes it look like he is already applying the squeeze to a resisting hero. Realistically, if you can tear steel like tissue paper, you should be able to tear an ordinary human body to a pulp faster than you can say the line. Instead, the villain just announces his awesome capabilities, but the fight goes on with compression of scale. Some heroes, like Spider-Man, like to say that they always pull their punches against weak opponents. This is somewhat convincing - it would be logical for them to do so - but it is interesting that the fights then play out exactly as they would if Spider-Man's punch just wasn't strong enough to overwhelm a human-level villain. In other words, in terms of how you would simulate this in a roleplaying game, Rationalization acts much like a special effect of Compression of Scale, with the special effect being that whenever a low defense character is hit by a big attack, he takes the usual amount of damage, then says "lucky I avoided 90% of the blow." And whenever a high offense character attacks a low defense villain, he rolls the usual amount of damage, then says, "good thing I pulled my punch, or that would have killed him." But otherwise, the fight goes on with the character exchanging blows according to the regular rules of the game.
Comic Book Coincidence: This is my term for a staple of comic books and many other media, the fact that the books are scripted so that heroes and villains without superhuman defenses are virtually never hit by bullets and other lethal attacks. The effect is really strong. Batman can dive through a hail of gunfire again and again and again without getting hit, but switch to punches or non-lethal energy blasts, and he gets quite often (he is agile enough to dodge most of them, but he still takes many hits). I often try to think of ways to model this, but I haven't seen this modeled in a published roleplaying games. That is, many games model the idea of comic book luck, but not the idea that characters are much luckier against bullets and swords than concussion blasts and fists. The closest is games that use fairly abstract damage such as hit points, then encourage you to think of hit point damage as just representing fatigue from avoiding close attacks. But this approach isn't very convincing when the game mechanics ignore it - when the unarmored character not only takes damage from being encased in molten lava, he is also immobilized and suffocating until someone breaks him out.
Harsh Reality: The advantage of the comic books is that, since they are totally scripted, they need not be consistent. The comic book writer is free to switch to harsh reality when desired for dramatic effect, then switch away when it becomes inconvenient. So many comic books which generally use compression of scale have some dramatic moments in which the true disparity of power levels becomes apparent. Sometimes this is used for comic relief - the hero seems so much mightier than the villain that instead of the writer trying to convince the reader that the villain can really provide a challenge, they just make him the joke for the issue. In any case, this relates to the general difference between highly scripted source material and freeform roleplaying games; you can't always match the source material unless your roleplaying game is also highly scripted. Of course, the more straightforward form of harsh reality is that some comic books, especially more modern ones, that just don't try to match the four-color feel at all, and combat really is pretty brutal and short unless both foes are very well matched. A game trying to imitate this form of superhero action wouldn't need to worry about the problems of scaling attacks and defenses.