I tend to think that Punisher's sales cratered because Castle became almost a parody of himself.
I don't disagree, but I see causation where you see correlation. From what I can tell, Castle became ridiculous precisely because his writers looked at every other writer ripping off his deal, and said to themselves, "Fuck it, we'll just make him even MORE extreme!!!" The problem is, that way lies NARM, or worse yet, leads to such desperation that you temporarily retcon Frank into a supernatural entity, because you honestly have no idea how to set him apart from all the guys who are ripping him off.
I mean, after all, how is Joe Schmuckatelli supposed to know that Spidey isn't a stinkin' mutie?
I actually agree with this, too - indeed, I distinctly recall us having this conversation in Japan, with me advocating this point of view - but with that in mind, the only two alternatives, from where I stand, are either a) allow mutants to make some progress, and develop their own cultural identity, beyond just being "stand-in for black/gay/Muslim victims of oppression," which Morrison came close to doing, or else b) give everyone in the Marvel Universe a lobotomy, so that they'll be willing to turn on even CAPTAIN FUCKING AMERICA as an "evil menace."
We see which alternative Marvel ultimately chose, and I suspect you feel the same way about it that I do.
I know that the reason for the 'hated and feared mutant' is that it's supposed to be a metaphor for intolerance as a whole, but it only works if the X-men were in their own universe. IMO
Again, I think I actually asserted this myself once, during a D&D session, and you're right, insofar as mutants continue to be portrayed as snakebit victims of every evil Klansman-level persecution under the sun, but I think there's room for more subtle discrimination in there as well, even as you continue to have screaming bigots. Rather than depicting the public as MONOLITHIC in their hatred of mutants, why not instead show the mutants as indelibly controversial no matter WHAT side you choose?
Hell, in THAT regard, mutants were Obama before his time. ;)