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topikt: I think you are simultaneously too knowledgeable and too naive. On one hand, hardly anyone involved in agriculture or manga-writing is aware that many of their problems are caused by capitalism, so you can't expect them to go around writing manga about it. On the other, if someone did do you really think it would get published in some major mainstream Japanese magazine? If the manga you imagine were written, we wouldn't be reading it.
(As to permaculture, I think it's strategically a dead end--nothing about any so-called permaculture I've seen advocated for seems culturally sustainable at all. People would get bored, try something more dynamic, that something would take over, permaculture gone. If you want change, it has to be to something most people would find better and more desirable than the status quo, something that can eat current deracinated capitalist culture; permaculture generally represents a step down for most people, so it's out.)