Googling just now there were a bunch of anti-American Beauty articles spurred by it turning 20 years old.
I'd think the biggest objections from kids these days would be that everyone is white and privileged and Kevin Spacey turned out the be a real life sexual predator. Also the way that plotline resolves, with her offering herself to him and him virtuously deciding it was the wrong thing to do, may be "problematic." And I guess we're not even allowed to laugh at him lusting after a teenage girl anymore.
The movie clearly doesn't encourage anyone to "screw a bitchy cheerleader" though, considering that he doesn't even do it and we're supposed to think that was the right thing.
If the movie had really expired two years after capturing the zeigeist like that I would have thought it would be more interesting for that 20+ years later then it probably is.
I never saw Man On the Moon, and I think it's forgotten. Would they have been able to make that if Taxi hadn't been on Nick at Nite?
Another movie from 1999 that we haven't mentioned yet and that I havent seen in a long time but that would probably still be in my top 2 or 3 from that year was Existenz.