You're confused by all your personal hangups. Yes, Prison School is trashy. That's not just "OK," that's the point.
Sorry, but there's nothing particularly ambitious about Prison School in the context of manga. Nearly-porn comedy is an actual subgenre, which includes titles like My Balls, Onani Master Kurosawa, and Itokoi Chidori, just to name the ones I've read. It might stand at the top of that particular world, and maybe it is even the best among comedies currently serialized, but it is still always able to rely on an existing and (this is the key point) commercially viable audience.
How can this be ambition? This is the exact opposite. The smut was a safety net in case the plot fell through.
On the other hand, with Me and the Devil Blues, he tried to adapt a historical figure and folk legend from a foreign culture that even the natives of that culture don't pay attention to. It is not just unique in the world of manga; it is unique in the entire world of sequential art. It may be flawed in its various ways, but I can excuse these flaws because the sheer audacity of serializing it in a ethnically homogeneous country with a reputation for racial insensitivity like Japan just outweighs everything else.
I can't believe you seriously brought up the Academy Awards in this discussion. Pretty much every films that won the award for best picture in the last two decades have been box office successes. You're really likening the mentality that warps the Oscars to our perception of Me and the Devil Blues? That Devil Blues is one of these multi million dollar grossers and Prison School is the comedy that got snubbed because it wasn't high brow?