While I agree with most of your points (Aren't you proud?), I tend to think that Punisher's sales cratered because Castle became almost a parody of himself.
Also, while I don't agree with much of what went on in Civil War, I've always maintained that the whole "all super-heroes being hated and feared" made more sense than singling out mutants. I mean, after all, how is Joe Schmuckatelli supposed to know that Spidey isn't a stinkin' mutie?
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