I mean it wouldn't be that hard to show people distrusting super powers. The avengers are heroes who saved the world on the grandest stage for the world to see in the first movie. Then with the incident on sokovia they're government threats and nearly considered public enemy. But mutants are a much scarier thought than a hand full of costumed public heroes. They're our sons, daughters, brothers, sisters, neighbors, teachers, pastors, co workers, they hide in the shadows, the sewers, etc. And all it takes is for them to introduce an instigator, a bigot who can tap into the worst of man kinds fears. It'd be a great reflection of today's America.
There are easier ways to introduce the origin of mutants without having to lean on the snap or the quantum realm. The eternals stuff would work nicely, but as far as actually introducing mutants Isn't it easier to introduce mutants by saying they've been around for ages? They were worshipped as gods, or existed as folk tales, mythical creatures, sewer monsters, circus freaks, internet hoax etc. But say maybe the population of mutants was and has always been very
small? That way when you introduce them, you could say out of 7 billion people on Earth mutants only make up maybe 50 or 60 thousand world wide and slowly growing. Which would make Xavier's mission to protect mutant kind and bring peace to their existence all the more important. The age of the internet and the age of heroes has brought them more into the lime light, but then we also get to see the ugly side of humanity and how they hate and fear some of these super powered characters, which in the mcu we haven't seen.
This kind of keeps people from saying "where have they been", they've always been there but they're sparse and have been hiding really well.