Franz Kafka, Amerika, The Trial, and The Castle. The trifecta as far as brilliant but imperfect manuscripts go. You know the details, death by burning rudely interrupted by good Uncle Max, who manages to make Kafka one of the most powerful authors, images, and ideas of the twentieth century. From words coined in his honor to bars in South Korea to novel and movie titles far and wide, part of our Kafkaesque existence includes our inability to escape the writer's influence.
Herman Melville, Billy Budd. Tell me this forgotten manuscript is not a novel. I dare you!
Thomas Pynchon, The Crying of Lot 49. Does Oedipa's character properly develop? Is he allowed to end it that way? Is it legal to include a long, tangential "play within the play" as early as chapter 3? Could the rumors be true he is rapping as the artist Tommy Pi? "This is America, you live in it, you let it happen. Let it unfurl."
I have a few others in mind, but I encourage you to add to this list.