Actually, "serious" music is in fact quite extensive in Japan. The reason why "manufactured" music is so prevalent is because 1) it's easy to produce, market, and make money, 2) the melody lines are usually simple and memorable enough for even the most tone-deaf to follow when it comes to social events like karaoke, and 3) mass media relies on them because they are easily recognized by a wide range of people. But those are all true in any other globalized culture.
But that doesn't mean "serious" music is hard to find in Japan. Serious jazz is arguably more popular in Japan than in America, oddly enough. Dive bars and local watering holes regularly feature excellent bands. The most reputable acts have sizeable followings and can afford to tour locally, and often regionally. Just like in other countries. And since Japan is tech-savvy, if you have trouble catching wind of these acts by traditional word of mouth, look to online reviews, recommendations, and sources like Facebook/Mixi/Twitter -- again, just like smaller bands promote themselves anywhere else. Or just walk into any record store and listen to some tracks.
Some artists I usually keep in my playlist: Soil & Pimp Sessions, Shiina Ringo and/or Tokyo Incidents, School Food Punishment, Soutaisei-Riron, Quasimode, Jazztronik, Shibasaki Kou, Natural High, Kyoto Jazz Massive, Jabberloop, Chatmonchy, Depapepe, Jill Decoy Association, Pizzicato Five, Zazen Boys, (and if you're up for a little electronic) Coltemonikha, Copter4016882, Plus Tech Squeeze Box, YMCK, Fantastic Plastic Machine, She.
If you haven't heard any of that, there's at least a decade's worth of back logs for you to work through as you get acquainted with the availability of "serious" Japanese music.
Really, the point is just not to throw out all Japanese-produced music as "fake, manufactured" j-pop.
