The problem with a story-by-story payment model is that it incentivizes publishers to focus on the headlines. It's also a bit tricky because people will only click on things that reflect what they want to hear. So even if an article is really well done, if it says something the majority of the population does not want to hear, good journalism will still die.
For an example, consider the Boston Globe's reporting of the child abuse cases in the Catholic Church [1]. There are many who violently disagree with the premise, so much so that they actively refuse to read or inform themselves about it. And you're expecting them to pay for it?
I'm also curious if there are any lessons learned from iTunes / Apple when they first started making individual songs in an album available for sale. Why buy an album of 12-15 songs for 10.99 when you can buy just those two good songs for 99c each? Do those artists still receive more sales? Is the overall effect more income for the music industry, or less?
[1]: http://archive.boston.com/globe/spotlight/abuse/betrayal/for...