What I liked most about Morrison's run (which 1. finally got me buying an ongoing title every month for the first time in five years, and 2. eventually left me totally fucking bored) is that he finally introduced the notion that people hate mutants not so much because they fear them, but because they envy them. Something I got pretty well twenty-three years ago, when I was thirteen.
The thing that's tough for me to swallow about the ongoing Claremontesque status quo (and again, this was hard to swallow even as a thirteen year old), is that there's no reason for the average Marvel universe citizen to be hip to the difference between a super whose powers come from an X gene, and one whose powers derive from a radioactive spider bite/ spider gene therapy/ experimentation by the Kree/Skrulls/you name it, and someone who belongs to a race of actual "gods."
In fact, if you want to know which is scarier, someone who can regenerate lost tissue insanely fast because of a scientifically improbable gene mutation, and someone who has built himself a suit of unstoppable mech armor, I find the vigilante with the suit of armor more terrifying by half.
The ongoing persecution of mutants, separate from the other superheroes (and it still is separate, even after Civil War) is something I was already finding silly before I'd stopped sleeping with stuffed animals.