I was never a big reader of the X-Men...the proliferation of X-titles in the 1990s was of the reasons I fled to DC (truthfully, I had been a DC child anyway) and then away from comics. But I recognize the basic characters and I see that the powers approach of my favourite games doesn't really reflect the X-Men as I understand them.
Caveats that I might be totally wrong in my understanding so that True Fans(TM) might object. However, this approach might be fruitful in figuring out how you do things to more accurately reflect the comics. It's mostly inspired by Marvel Heroic Roleplaying (it's not influenced by AMP except for what was in the podcast; I don't own AMP and haven't read it).
When I look at them, the characters in the core X-Men and the New Mutants (again, circa the late 1980s and the early 1990s, when I was occasionally looking at the books) are mostly human but with one or two powers that make them different. As humans, they're usually pretty good...Scott Summers is well-trained, Warren Worthington seems to be buff, Kitty Pryde manages well, and so on. (In story, the justification is the danger room and the training.) It's not until later (such as in Excalibur) that you see any disabled heroes. Anyway, the powers are applied differently: a character might freeze a lock or throw iceballs or make an ice wall, but it's one power. We'll call it a theme. This is like the power sets in Marvel Heroic Roleplaying. (I don't have a list of themes handy, but I might edit one in later.)
Both Supers! and ICONS have mechanisms to handle this stunting: Competency dice and determination points.
First, we roll to see how many themes you have. We're going to use 2d6 because we want the bell curve.
|Roll||Number of themes|
|2-6||One power theme (Colossus has the Strength theme; Angel can fly; Cyclops blasts things with his eyebeams)|
|7-10||Two power themes (Kitty phases and is smart; Wolverine has the healing factor and an animal theme)|
|11-12||Three power themes (I can't think of examples at this second, but I'm sure they exist. Maybe Cable, who has cybernetics, and the telekinesis, and being from the future and having that kind of knowledge might qualify as a third--I don't know enough about the character to be sure.)|
Then we're going to figure out the width of your biggest theme. This is the number of standard expressions of your power. Iceman lucks out because he has three main expressions: ice armor, movement, and the ability to create things out of ice. Colossus has two expressions: strength and durability. (You might be able to call that one in ICONS with Alternate Form.) Cyclops and Angel have a single expression: optic blasts and flight, respectively. (Actually, you could make an argument that Angel's second theme is wealth but I'm not sure I want to go there. Worth considering that wealth might be a power, like any ICONS ability over 6.)
Again, we roll 2d6 for the bell curve:
|Roll||Width of theme|
|2-6||One main expression|
|7-10||Two main expressions|
|11-12||Three main expressions|
If you have multiple themes, the additional ones only get one main expression. (That's okay: you can stunt on any of these themes.) You get to pick which one might have multiple expressions, if any. You can run all of those main expressions at once. So Iceman, who has three main expressions, can have the armour, the movement, and the attack.
You pick (or roll, on the nonexistent table) your themes. Once you have themes, you can pick or roll main expressions. Those are the powers you normally use, but you can stunt others.
"Great," you say. "But what is the point?"
The point is that it's free to swap expressions or powers within your main theme. (In systems with a finer grain, such as Mutants & Masterminds, you might say that swapping within your theme takes a bit of time, maybe your movement action, but doesn't cost hero points.) To keep extra expressions up simultaneously costs a competency die or a determination point. To stunt in some other theme costs a competency die or a determination point. It costs two dice or points to bring a power into your theme, and you have to have a justification.
By defining the themes, we get to ones where it's difficult to use a power (it's from a different theme according to the homebrew rules we've just put down). In fact, you can have character generation being constructing your theme, or players can add to the theme with experience. (That's certainly the only way to add powers or expressions to a secondary theme.)
Themes would include a particular animal or being animalistic; darkness; force; light; air; earth; water; fire; plants; movement; telekinesis; mental; decay or corruption; magic; strength; time; body alteration; and so on. A theme has one or more obvious main powers and the set of things that often go with it. A theme has, oh, five to ten powers in it--we're looking for comic book cliches here. Some of them will be contradictory...just don't take them both.
|Air||Flight or Gliding, control winds, shielding winds, alternate form (air), gentle fall, shielding|
|Animal theme||Depends on the animal...Power mimicry specific to animals, Flight, Swimming, Burrowing, Leaping, Claws/fangs, Strength/toughness, Growth/Shrinking, Super-senses (smell, taste, hearing, eagle eyesight, 360 degree vision, sonar, infrared vision, electroception)|
|Body alteration||Growing, Shrinking, Phasing or Intangibility, Air walking, Density Increase, Duplication, Regeneration, Enhanced Senses, Stretching or Malleability|
|Mental||Mind reading, Mental link, Mind control, Mental blast, Mind find, Possession, Telekinesis, Precognition|
|Phasing||Intangibility, Air walking, Enhanced senses, attack by phasing through things, disable electronics|
|Strength||Strength, Invulnerability, Leaping, Flight, Superbreath, Alternate form that gives strength, Density Increase, Immobility|
A given power can show up in more than one theme. There are multiple ways of doing an energy blast: that was the whole point of going to effect-based powers. Here I'm trying to graft a cause back on to those.
Themes might possibly be the character types in the Mutants & Masterminds random character creation system. In Champions terms, everyone gets an elemental control and the ability to stunt within it for free.
This is totally untested, but I think it might work.