There were ticky-tack fouls back then. You can find highlights of Jordan's big games against the Pistons where they show fouls and FT's. He got all the calls.
One thing that has changed is the crackdown on flagrant fouls, but that's good. Flagrant fouls are not good basketball.
Another big change is no hand checking, which I think is a good rule change too. Not only does it open the game up more, but it requires better defensive skill. You have to be some combination of long, quick, strong, and having good footwork in order to keep your man from getting to the basket. Guys today would just goad you into fouls if there were hand-checking, so it'd mean more FT's and more boring BS.
Jordan was smoking tiny little dudes like John Starks, Joe Dumars, Byron Scott, and Jeff Hornacek deep in the playoffs. Dumars was a good defender for a little guy but he was still a little guy and that matters a ton. The Warriors dynasty alone had 4 very good, big wings they could have put on MJ. Most playoff teams have at least a couple.
Another big change is you can play zone D, which I think is good.