Mystique from X-MenRecently, The Frogger and I were watching X-Men: The Last Stand (aka X-Men 3: Mutants Doing Ridiculous Wire-Work Stunts), which should get you thinking about what mutant powers you would like to have.  Unfortunately, I'd already thought this through in some detail (control of gravity, take a minute to think through the relativistic implications and tremble Homo sapiens).  So, I had time to ponder grander thoughts, like how the hell do they get those mutant powers?  Actually, if one pays attention (I find that a naked, blue, reptilian Rebecca Romijn helps one focus), one can infer a fair bit about X-Men genetics with only some vigorous bending of one's suspension of disbelief (provided that you are cool with ignoring the laws of physics).
  

SUPPRESSING THE X-GENE The Last Stand
What We Know: The effects of a mutated X-gene can be suppressed by treatment with an antibody derived from the mutant child Leech.

How We Know: It's only the major plot device of X-Men: The Last Stand.

What This Means:  Suppression of the  X-gene's effect by a single antibody suggests that the X-gene exerts its effects through a single protein product.  The general mutant effects of the X-gene are probably due to changes in expression level, not change in function, because reducing the amount of active X-gene product makes mutants normal.  Specific powers may be related to differences in X-gene function.  The suppressive effect of the "mutant cure" is should wear off over time as the antibody is depleted (e.g., "cured" Magneto rocking a chess-piece's world in the final shot of X-Men: The Last Stand).  Leech probably does not have a mutant X-gene, because the antibody does not negate his own power.

DISTRIBUTION OF MUTANT POWERS The Last Stand
What We Know: Mutant powers are classified by strength from 1-5, with 5 being the strongest and the rarest.  Frequency of a class decreases as the powers get stronger.

How We Know: In X-Men: The Last Stand, Callisto tells Magneto that Jean Grey/Dark Phoenix is a Class 5 mutant, stronger than any other she has ever sensed before.  She also indicates that mutants above a Class 3 are rare.  This implies that mutants become progressively more rare as they become more powerful.  

What This Means: This means that the mutation effect size follows an exponential distribution (i.e., larger effects are much more rare than small effects).  This is the same type of distribution that scientists expect for real mutations in real genes.

MUTATION RATE The Last Stand
What We Know: Mutant powers are caused by mutations in the X-gene 

How We Know: For starters, Stan Lee said so.  This repeat this information is repeated in X2 to Iceman's family.

What This Means:  In humans, the probability of mutation is on the order of 10-9 per base pair.  Given a reasonable guesstimate of the size of the X-gene, we should expect no more than a few thousand mutants in the United States.  The X-Men trilogy strongly implies that there are far more mutants than this estimate.  Mutation rate, however, is variable across the genome.  The ending of X2 implies that the rate of human evolution (likely meaning the amount of variation in the human population) has suddenly increased.  The mutation rate of X-gene may be orders of magnitude higher than the rest of the genome, probably due to BPA, nuclear power, MSG, microwaves, vaccines, George W. Bush, the decline of the traditional family, global warming, FOX canceling Firefly, etc.

INHERITANCEWolverine, Iceman, Pyro, and Rogue from X-Men 2 (EW.com)
What We Know: Mutant powers are inherited from the father.

How We Know: In X2, Pyro tells Iceman's family that its the dad's fault their son is weird.

What This Means:  Normally, we think of things only being inherited from the father when the gene is located on the Y-chromosome, as this is the only uniquely male DNA floating around.  Females are XX and males are XY.  If the X-gene were on the Y-chromosome, there should not be any female mutants.  X-inactivation of the mother's X-chromosome would allow a daughter to inherit their mutant powers from their father, but the sons would inherit their mutant powers from their mothers (son's X-chromosome always comes from Mom).

Of all the things in the X-Men trilogy, this is what ruins my suspension of disbelief?  I need to get out more.