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In a couple of his movies, the bad guys are people who take "just doing their job" too far.
Parents are usually depicted as well-meaning, but generally out-of-touch and ignorant.
This is played with in Ferris Bueller's Day Off, where, yes, the adults are easily fooled and/or moronic...but the kids are easily fooled, too.
The Breakfast Club hit this one in a somewhat dark way. Not only are there no positive adult characters in the movie (save Carl the janitor), almost all of them are downright cruel and abusive. That attitude is summed up pretty well in Allison's line, "When you grow up, your heart dies."
All There in the Manual: Hughes apparently spent several years putting together a detailed history for the Shermer universe of his films (see below), but his stories and notes have never been released. A lot of it wouldn't match up, anyhow (see The Verse below).
Getting Crap Past the Radar: Some of his earliest films (from before the PG-13 rating was introduced) managed to sneak by with a PG rating, even though their content should obviously have been rated R.
Monochrome Casting: Virtually none of his movies had a non-white lead. Justified, since most of his stories took place in American suburbia, which was still not quite integrated when he began writing.
Society Marches On: Looked at objectively and from current standards, Ducky from Pretty In Pink is a real creep, not to mention the dean of students turning a blind eye at what he believes to be father-daughter incest in Ferris Bueller's Day Off.
Something Completely Different: Weird Science is the odd man out among the teen pics, being much more fantasy-based and a little cruder in its humor than the others.
John Hughes: When I started making movies, I thought I would just invent a town where everything happened. Everybody, in all of my movies, is from Shermer, Illinois. Del Griffith from Planes, Trains & Automobiles lives two doors down from John Bender. Ferris Bueller knew Samantha Baker from Sixteen Candles. For 15 years I've written my Shermer stories in prose, collecting its history.
It's long been speculated that Pretty in Pink, Some Kind of Wonderful, and Home Alone also take place in the Shermerverse, since those movies were written (but not directed) by Hughes and feature similar themes. Adding on to that, there is mixed evidence that Uncle Buck and Curly Sue (both directed by Hughes) might take place in the Shermerverse, but this hasn't been confirmed.
Weird Science explicitly takes place in Shermer (Lisa is seen teaching the Shermer High gym class at the end), though it has its own Speculative Fiction internal logic that is inconsistent with the other canon Shermerverse movies.
She's Having A Baby does NOT take place in the Shermerverse, since Neal Page's wife is seen watching that movie on television in Planes, Trains and Automobiles.