I'm not sure I find iconic villains problematic, so much as iconic villains who kill. I can handle characters like Riddler or the Penguin or Sandman, Vulture, etc etc returning time and time again and never being offed, but when you reach the levels of unrepentant killing of someone like the Joker, it's a lot harder to justify.
it's want reason why I heartily dislike making villains by default psychotic killers. The villains who don't coldbloodedly kill are far more interesting to me and I welcome their returns far more readily than someone like the Joker who's now got to the point where even comic book realism is stretched by the idea he's not constantly incarcerated or dead at the hands of a citizen or cop, if not a hero.