Take the idea of Quality, for example. Pirsig talks about it for half the book; this is a concept that drives him insane and is central to his life and to the narrative. I still haven't the foggiest idea of what he is talking about, pages of strange analogies notwithstanding.
To me, this was a book about a troubled intellectual and his grappling with mental illness. About somebody that drives himself insane by obsessing over abstruse concepts arising from human experience. And it's a well-told story that made me think, but also made it very hard to relate to the protagonist simply because I do. not. understand. his intellectual struggle.