People and systems are depicted in fiction as stupid because writers, by and large, are stupid people.
In reality, the problem isn't that writers are stupid but that writers are lazy--unfortunately the result is effectively the same.
Writing a smart character takes a great deal of work. Most authors simply will not put in that work.
Guy Gavriel Kay is one of the few authors I like simply because his characters are competent.
Writing characters that are actually intelligent is really, really hard and I tend to remember the few characters that seem honestly clever that I really tend to remember those. I still remember my jaw dropping when L first told Kira he was coming after him in Death Note because of the clever way that was executed. Not to mention how both of those characters exhibited a very different sort of intelligence and you could follow their reasoning process most of the time.
Where Japanese writers suffer is, not unlike the American TV show writer, in the business incentive to drag a series out for as long as possible to milk the most money out of it. Anyone would run out of material under those circumstances. The best serializations are those smaller ones that either planned the arc of the story from the beginning, or never pretended to have one in the first place.
http://www.imdb.com/title/tt0978076/
The first episodes with the Teacher are okay, but it really kicks into high gear when they being playing 'minority rules' later on. Really marvelous!
If you enjoy a real challenge read The Book of the New Sun by Gene Wolfe. It's the most rewarding puzzle I've ever tangled with. I was up for days, weeks, thinking about it afterwards.
Here is an introduction by Alastair Reynolds.
https://www.youtube.com/watch?v=-0kY1kJA0jA
It is the favorite book of a huge number of well known authors but is less known outside of their circles.
Wolfe's book is a riddle wrapped in a mystery inside an enigma.