BUT, we as writers must trust that the reader is able to judge the story as a whole, eventually, because the alternative, leading someone through 300 pages of smooth-flowing prose only to reveal a story void of quality ideas is...sucky.
The idea. Coming up with a good idea is something writers often forget to do. I say this because I've read at least 300 short stories in 2009, and many times a piece will impress me until I stop to actually think about it. And, sadly, I often don't bother to come up with good ideas myself. My desire to write is so strong that I just want to get words down on a page, and then my drive to make those words engaging pushes me to revision, and before I know it, I have spent two years (or seven) polishing a book that doesn't have that critical good idea at its center.
What do I mean by a good idea? That depends on what you are writing about. A love story, for example, won't be an interesting story if the love isn't interesting. Even if it's written in beautiful prose, mundane love will feel mundane. Or, if one is writing a story about a criminal mastermind who tries to steal the nose off of the Statue of Liberty, a pathetic plan to get that nose (a really big saw!) won't feel satisfying. (Okay, okay, unless you're going for some sort of irony.)
If my own writing practice is any indication of other people's writing practices, we are not spending nearly enough time on developing that initial good idea--or the other good ideas required throughout a story. And, a dumb idea garnished with a grand sprig of parsley will only impress for so long. Eventually, the leaf gets lifted.
So, I'm sorry. I'm sorry because the FIRST thing we need to work on, the thing that takes the most brilliance, is the LAST thing a reader will see, if they ever see it at all. And, I'm sorry that pushing yourself so that the heart of your story is solid doesn't necessarily result in a reader's recognition that your writing is good when they are browsing through your book before committing to read the whole thing. A solid foundation is necessary to write a good book, but that good book will often be judged by its adornments. Still we press on, hoping that someone will see our vision and heart. And, our ultimate goal is to make everything exquisite, so that the lovely prose does not cover for a bad idea, and the good idea is not hidden by bad prose.