The entirety of Marvel's characters (at least the interesting ones) have been listed here
Some sources say the total number of characters in Marvel is somewhere between 8,000-15,000 characters. Some of these might not have powers as per your definition of them, but I don't know why you have those limits (Iron Man if stronger than some mutants with his suit). Either way, there are many characters in his count who are in fact normal human beings. Also, some of those characters aren't even from Earth even though they do have powers. So just for argument's sake let's take the low number from those estimates of 8,000 people.
Now if we assume 616 has a population comparable to ours, say roughly 8 billion people. If we assume that 8000 of them have powers of some sorts that's about 1 person in every million, or about 0.0001% of the population. If you were instead to assume the highest number of 15,000 that would still only mean about 2 people for every million, so the difference isn't high.
That's really no so much is it? As an added bonus, this would also mean that a city like New York with about 8 million people, should only have about 8-16 powered individuals. 616's New York obviously has more, but that is likely an artifact of New York being a cultural hub in the 616 universe as it is in ours. After all, in our universe as well, New York is home to a large amount of actors, singers, artists, CEOs etc. That's far above the normal proportion of these people almost anywhere else.