But you're missing something. Despite what comics might have stated with there only being 16 million mutants in the whole world there is no way that that number was anywhere close to accurate. Just think about it, mutants were forming their own ghettos and equivalents of china towns in New York City and maybe other big cities and there was an X-Corporation branch in most of the major cities of the world. If there were enough mutants for all that then there had to be way more than just 16 million spread all across the world. 16 million would have been less than 1 percent of the whole world's population. And it wasn't the number of mutants in US alone but in the whole world. So there's no way that it matched what was being shown in the comics themselves.
And what comes to Marvel's decision to drop the mutants to 200 I don't agree with it one bit either. There was no need for that and if they wanted to cut the number of mutants they could have done it in another way and didn't have to go with the endangered species direction. But I do believe that people like Quesada felt that there were too many mutants in the whole MU and decided (at least partially) because of that to wipe most of them away. I think that the idea to make mutants endangered only came after that. Probably someone came up with that direction once it had already been decided that the mutants would be cut down in numbers. That direction could have IMHO been a decent standalone story if it was a thing for only a couple of years instead of 7 years!
So as i said I don't agree with it or defend it but I do believe that the original main reasoning for it was that there were too many mutants. And I can see why they would feel that way when it comes to books with non-mutant characters. A real superpowered minority that is as big as the number of people with Chinese, Indian or African decent in the real world could be a great story but it would never be possible in a shared MU.
Especially now that X-Men are not even the most important part of that MU in Marvel's opinion. But that once again goes to the territory of asking if mutants and X-Men should be in their own world separate from the rest of MU and it's a discussion I'm not really interested in participating again because there are pros and cons to that just as there are to the shared MU.