I think it was an okay move to stop showing popular heroes smoking (wolverine, gambit, nick fury, the thing, etc.), but they should've let the villains keep smoking. We're already NOT supposed to root for them in the first place (no matter how cool they are), and you can easily show others around them bothered by the smoking. Seriously, who's looking up to Kingpin, Bullseye, or Sabertooth??
As for bringing it back, doubtful at this point. Real life example: Yes, we still see smokers out in the world, but nearly all of them have to do it away from buildings or at home. Either way, away from the general public. J. Jonah Jameson wouldn't be smoking in his office (he'd be fined or potentially sued) and Reed Richards definitely wouldn't be smoking around all those kids they take care of. It's very realistic to not show it if it doesn't involve low level criminals at the docks or something.