I believe Mutations can be categoried using the class 5 system.
Class 1 Mutations: Cosmetic mutations that serve no purpose or mechanical function. Examples would be unusual eye color, hair color, skin color, and voice.
Class 2 Mutations: Physical mutations, usually kept within the normal realm of the animal kindgom. Examples would be natural weapons (claws, fangs, horns), natural armor, enhanced senses (low-light vision, darkvision, scent), and any other naturally occuring physical trait that can be found in the animal kindgom that is not normally something humans have. Enhanced strength, speed (within the limits of what is physically capable), and intellect would also fall into this category
Class 3 Mutations: Physical mutations that fall outside the norm even within the animal kingdom. Examples would be rapid cellular regeneration, skin that mimics inorganic material (rock, metal, diamonds), production of biochemical agents (acid, poisons, pheromones), non-mamilian traits (such as plant traits, undead traits, construct traits).
Class 4 Mutations: Metaphysical mutations that allow the subject to do something not normally feesible, but within a limited constructed realm. Examples would be telepathy, telekinesis, empathy, energy projection, elemental manipulation, teleportation, enhanced speed (within the limits of what is not physically capable), subjective directional gravity, and many more.
Class 5 Mutations: A class 5 mutation is simply a class 4 mutation with no upper limit. Someone with a class 5 mutation could feesibly do anything they could imagine with their power. Because such powers are beyond the mechanical scope of any system, such powers should be limited to NPC characters or given access to a PC character only when they temporarily become a GM character. Such characters usually are consumed by their power and may develop unfortunate mental disorders due to the scope of their abilities. For this reason, it would be strongly recommended class 5 mutations be heavily limited.
For example, a player might have access to the class 4 mutation of elemental manipulation (water), but he can say his character is going to push himself beyond his safety limits (becoming a GM character and subject to the consequences of his actions). He might state an overall goal for his character (holding back a flood from destroying the town his party members are trying to evacuate), but the GM might role-play trying to hold back a force of that side might "consume" the player's character as he loses himself to his power. Such a trade off might result in the ultimate sacrifice of the hero, or he might be able to pull himself back within the limits of his powers before it consumes him (after his party gets the last of the civilians to safety, of course). Either way, some mechanic would have to be put into place to prevent a power hungry character from abusing his abilities without fear of death. Sometimes, no matter how noble the cause, you have to die to be a hero.
These 5 classes of mutation are just to help visualize what would be required for each type of super hero character. Obviously class 1 mutations require no real mechanics, and someone could simply say as part of their background they are a class 1 mutant. This would allow them to fit into a mutant (more along the lines of x-men) heavy campaign without having to invest character resources (talents, powers, feats) in a mutation mechanic if they do not specifically want one. Class 2 and class 3 mechanics could be done with a combination of enhancements and feats. It would be simple enough to say, okay... you have claws, so when you use those with your Unarmed Attack skill you deal slashing damage instead of bludgeoning damage, but other physical mutations might require a little more work. Class 4 and 5 mutations will probably be contained completely in the realm of enhancements and FX powers.
Without really doing any mechanical legwork, what do people think?
"Things will get better. Then they will get worse. Then they will get better again. Just remember, if it's not good, than it is not the end."
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