By in large, I think the majority of jRPGs could stand to "grow up" a little, and not superficially (tits, ass, guns, bathroom philosophy). When I played Mass Effect 2, I never felt like I had to overlook some aspect in order to enjoy it (save, maybe, the final boss). But even in my favorite jRPGs, I find myself having to turn a blind eye to some aspect or part of the game, in order to not feel dumber for having liked it. Either the story becomes rediculous and pretentious (FFXIII), or your faced with one or two really annoying characters that don't fit in (bratty children... or adults). Sometimes I think jRPGs try too hard to be smart or clever. To be clever, you actually haveto be clever... not pretend that you are!
That said, Western games aren't perfect either. Red Dead Redemtion had a lot of groaner annoying characters that I would expect more to come from a jRPG. And the Assassin's Creed series has similar problems to many jRPGs of swinging into "WTF Religion!" territory.
BTW: Leyvieur, you're response was absolutely right, I should have specified "console". I was just thinking Planescape Torment and LucasArts when I said "obvious exceptions", but I should have specified that we were talking consoles specifically.