In Three Things to Unlearn from School, Ben Casnocha cites Bill Bullard's list of three bad habits of thought: Attaching importance to personal opinions, solving given problems, and earning the approval of others. Bullard's proposed alternatives don't look very good to me, but Bullard has surely identified some important problems.
I can think of other school-inculcated bad habits of thought, too many to list, but I'll name two of my least favorite.
I suspect the most dangerous habit of thought taught in schools is that even if you don't really understand something, you should parrot it back anyway. One of the most fundamental life skills is realizing when you are confused, and school actively destroys this ability - teaches students that they "understand" when they can successfully answer questions on an exam, which is very very very far from absorbing the knowledge and making it a part of you. Students learn the habit that eating consists of putting food into mouth; the exams can't test for chewing or swallowing, and so they starve.
Much of this problem may come from needing to take three 4-credit courses per quarter, with a textbook chapter plus homework to be done every week - the courses are timed for frantic memorization, it's not possible to deeply chew over and leisurely digest knowledge in the same period. College students aren't allowed to be confused; if they started saying, "Wait, do I really understand this? Maybe I'd better spend a few days looking up related papers, or consult another textbook," they'd fail all the courses they took that quarter. A month later they would understand the material far better and remember it much longer - but one month after finals is too late; it counts for nothing in the lunatic university utility function.
Many students who have gone through this process no longer even realize when something confuses them, or notice gaps in their understanding. They have been trained out of pausing to think.
I recall reading, though I can't remember where, that physicists in some country were more likely to become extreme religious fanatics. This confused me, until the author suggested that physics students are presented with a received truth that is actually correct, from which they learn the habit of trusting authority.
It may be dangerous to present people with a giant mass of authoritative knowledge, especially if it is actually true. It may damage their skepticism.
So what could you do? Teach students the history of physics, how each idea was replaced in turn by a new correct one? "Here's the old idea, here's the new idea, here's the experiment - the new idea wins!" Repeat this lesson ten times and what is the habit of thought learned? "New ideas always win; every new idea in physics turns out to be correct." You still haven't taught any critical thinking, because you only showed them history as seen with perfect hindsight. You've taught them the habit that distinguishing true ideas from false ones is perfectly clear-cut and straightforward, so if a shiny new idea has anything to recommend it, it's probably true.
Maybe it would be possible to teach the history of physics from a historically realistic point of view, without benefit of hindsight: show students the different alternatives that were considered historically plausible, re-enact the historical disagreements and debates.
Maybe you could avoid handing students knowledge on a silver platter: show students different versions of physics equations that looked plausible, and ask them to figure out which was the correct one, or invent experiments that would distinguish between alternatives. This wouldn't be as challenging as needing to notice anomalies without hints and invent alternatives from scratch, but it would be a vast improvement over memorizing a received authority.
Then, perhaps, you could teach the habit of thought: "The ideas of received authority are often imperfect but it takes a great effort to find a new idea that is better. Most possible changes are for the worse, even though every improvement is necessarily a change."
It was certainly modeled after the Prussian style schools, so it was designed in a certain sense. That a group of movers and shakers actually sat down and said "this is how we want our schools to be and why, what can we do about it?" seems far fetched to me, but not impossible. More likely the Prussian style was much more impressive, and politicians pushed for it without regarding whether or not it was actually a superior system.
The Prussian system was specifically designed to replace the local aristocracy by instilling obedience in the crown through indoctrination. It was one of the primary goals, the other being preparing the population with skills needed to operate in an industrialized society - namely reading, writing and arithmetic.
I don't believe the American version of the same was as focused in its goals. There was no single entity that could drive such goals (we had no King), so it seems unlikely that the Whigs (the major proponents of the system) were trying to indoctrinate students into supporting the Whig party. I think it was more generally thought of as a more efficient way to educate children.
The general effect is that students learn to do as they are told by whoever is in authority, so much so that this has become a virtue. In contrast, questioning authority was one of the founding principles of the country. Since the old system was community driven, often with one teacher teaching all subjects for all ages, the students were required to learn some things for themselves, and often also required to teach younger students what they knew.
Also, just because an agreeable workforce was a goal does not mean it actually succeeded. In general, however, I think it has done a reasonable job - much better than allowing students to think for themselves would have.
I'm somewhat familiar with education in the U.S., and I perceive a lot of heterogeneity. Public schools vary widely, to say the least. Aside from that, there are alternatives such as parochial schools and home schooling.
I'm not so familiar with schools outside the U.S. Which modern systems would you say are less authoritarian than the prevailing U.S. system?