Bundles and ads have an advantage that micropayments don't have: they allow popular but unimportant stories to help finance the important but less lucrative ones.
For instance, in the old days when newspapers were all made of actual paper, the sports section helped finance investigative journalism that was really expensive, but often far less popular and that sometimes led to dead ends.
So without bundles or site-wide ads whose revenue is shared for all stories, sports and gossip writers would rake in most of the cash while the really important investigative journalism would struggle to survive.