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mug3n: As they say "sex sells", that's really the main reason this exists even with such a mediocre semblance for a plot. Even though I would argue that in general manga have terrible plot on average, and the only reason this stands out is because people are very sensitive to sexual topics. You could swap in the ecchi part with fighting, or 100 chapters of back and forth "romance" and you'd get your generic mediocre shounen.
Also while I do get where you're coming from, concerning your point that a person is better off reading hentai, I believe that's oversimplifying things. People actually do appreciate erotic entertainment that's not simply sex.
Granted, I fully agree that a good plot with "naturally" occurring sex scenes is better. Actually scratch that, at the end of the day it's the plot that makes the difference. Sex, fighting, romance, premise is only secondary as long as an author can create a believable, interesting, and consistent plot. You can have a great plot with the dumbest premise imaginable as long as the author knows how to write, and you can have a terrible plot with the most amazing premise if the author has no idea what he's doing. Sadly manga authors fall mostly in the second category (and even then the premise also sucks or has been overdone to death mostly).
Stereotypes and cliches are preferred over originality, but considering that such works sell, it means that there are readers happy with this type of quality. I believe a very good example is the isekai genre: very formulaic, appealing to the reader's ego and basic desires. But it sells, very well at that. Now compare this to some of Asano Inio's works let's say. Few people want to read about depression, misery and real life in general. The main issue with "quality" plot is that it usually cannot be appreciated by a large enough audience(= lower sales) and it's also a "risk" to the publisher, since by its very nature it is original. A lot more can be said about this, but I hope you get my idea - the problem you see here is rather a problem inherent to the current manga industry in general.