When it comes to getting an acceptance, there are a lot more factors than just "is the writing good," variables that have absolutely nothing to do with the quality of the writing or how "in touch" the editors and agents are with the reading public. The underlying assumption to your statement, that if writers who write good stories aren't getting published, then there must be something wrong with the system, is awfully close to the statement "no one appreciates my genius."
Is writing an art? Yes. It writing a craft? Yes. But publishing is a business and it is very important to realize that. In a business, it's not just how good your product is. It's also about matching the market's needs, the consumers desires, and understanding that there's only so many factories to produce so many widgets each year and only so many different types of widgets that the stores are willing to stock in order to meet the needs of their customers.
There's also more to writing a publishable manuscript than just stringing sentences together and making likable characters. At a deeper level of the story you have to be able to answer the "so what?" question. Even if the story is just written for entertainment purpose, their needs to be a deeper reason for the reader to care.
Lori has hit the nail on the head here. Spot on. Great post.
JJ
