I'm suspicious of this theory that thirteen-year-old kids are intrinsically messed up. If it's physiological, it should be universal. Are Mongol nomads all nihilists at thirteen? I've read a lot of history, and I have not seen a single reference to this supposedly universal fact before the twentieth century. Teenage apprentices in the Renaissance seem to have been cheerful and eager. They got in fights and played tricks on one another of course (Michelangelo had his nose broken by a bully), but they weren't crazy.
As far as I can tell, the concept of the hormone-crazed teenager is coeval with suburbia. I don't think this is a coincidence. I think teenagers are driven crazy by the life they're made to lead. Teenage apprentices in the Renaissance were working dogs. Teenagers now are neurotic lapdogs. Their craziness is the craziness of the idle everywhere.
When I was in school, suicide was a constant topic among the smarter kids. No one I knew did it, but several planned to, and some may have tried. Mostly this was just a pose. Like other teenagers, we loved the dramatic, and suicide seemed very dramatic. But partly it was because our lives were at times genuinely miserable.
Bullying was only part of the problem. Another problem, and possibly an even worse one, was that we never had anything real to work on. Humans like to work; in most of the world, your work is your identity. And all the work we did was pointless, or seemed so at the time.
At best it was practice for real work we might do far in the future, so far that we didn't even know at the time what we were practicing for. More often it was just an arbitrary series of hoops to jump through, words without content designed mainly for testability. (The three main causes of the Civil War were.... Test: List the three main causes of the Civil War.)
And there was no way to opt out. The adults had agreed among themselves that this was to be the route to college. The only way to escape this empty life was to submit to it.
Teenage kids used to have a more active role in society. In pre-industrial times, they were all apprentices of one sort or another, whether in shops or on farms or even on warships. They weren't left to create their own societies. They were junior members of adult societies.
Teenagers seem to have respected adults more then, because the adults were the visible experts in the skills they were trying to learn. Now most kids have little idea what their parents do in their distant offices, and see no connection (indeed, there is precious little) between schoolwork and the work they'll do as adults.
And if teenagers respected adults more, adults also had more use for teenagers. After a couple years' training, an apprentice could be a real help. Even the newest apprentice could be made to carry messages or sweep the workshop.
Now adults have no immediate use for teenagers. They would be in the way in an office. So they drop them off at school on their way to work, much as they might drop the dog off at a kennel if they were going away for the weekend.
What happened? We're up against a hard one here. The cause of this problem is the same as the cause of so many present ills: specialization. As jobs become more specialized, we have to train longer for them. Kids in pre-industrial times started working at about 14 at the latest; kids on farms, where most people lived, began far earlier. Now kids who go to college don't start working full-time till 21 or 22. With some degrees, like MDs and PhDs, you may not finish your training till 30.
Teenagers now are useless, except as cheap labor in industries like fast food, which evolved to exploit precisely this fact. In almost any other kind of work, they'd be a net loss. But they're also too young to be left unsupervised. Someone has to watch over them, and the most efficient way to do this is to collect them together in one place. Then a few adults can watch all of them.
If you stop there, what you're describing is literally a prison, albeit a part-time one. The problem is, many schools practically do stop there. The stated purpose of schools is to educate the kids. But there is no external pressure to do this well. And so most schools do such a bad job of teaching that the kids don't really take it seriously-- not even the smart kids. Much of the time we were all, students and teachers both, just going through the motions.
In my high school French class we were supposed to read Hugo's Les Miserables. I don't think any of us knew French well enough to make our way through this enormous book. Like the rest of the class, I just skimmed the Cliff's Notes. When we were given a test on the book, I noticed that the questions sounded odd. They were full of long words that our teacher wouldn't have used. Where had these questions come from? From the Cliff's Notes, it turned out. The teacher was using them too. We were all just pretending.
There are certainly great public school teachers. The energy and imagination of my fourth grade teacher, Mr. Mihalko, made that year something his students still talk about, thirty years later. But teachers like him were individuals swimming upstream. They couldn't fix the system.