Given the intent behind the movie (and far more obviously behind the novel it originates from, which is a lot more explicit about its message, and much, much better than the movie), a lot of irony and a solid dose of absurdity was to be expected.

The movie makes a lot more sense to Japanese and people who know modern Japanese culture well. It's a sci-fi fable both observing and denouncing (via the absurb) the Japanese dislike for anything that doesn't fit a rigid social mold, some aspects of the extremely rigid and exacting school system, the cult of authoritarism, the cult of extreme violence and other things etc.

You're far from the only one who took it at another degree and saw an action-gore fest with absurdities and plot holes That's one reason it got censored or forbidden in many countries, because it's such a Japan-centric thing and to others it seems to be just a violence showcase for a teenage audience thriving on hyper-violence. Even in Japan the message of the movie got evacuated by many and it turned into one more popular gore movie (and its sequels etc.). It's a fairly mean, and fairly cynical (yet often funny, IRRC) boo criticizing aspects of modern Japan. The movie is at best half succesful at conveying the messages (an even the plot, IRRC) of the book (the movie's been compared to the similar "failure" of O. Stone with Natural Born Killers).

It's meant to be a kind of Japanese 1984 or Brave New World. Well, not exactly that, but a book in the tradition of these.

At the first degree yeah, it's absurb, over the top and has many plot holes.