The NYT lists have always been skewed by paid promotion... and the new ebook lists will also favor promotion through the traditional markets.
Suppose, for example, that I hit a ball out of the park and sold 10 million copies of a book... through my own website? NYT will never see those stats, and I won't be on their list. Only if I sold well through one of their traditional channels (existing publishers and booksellers, or now, Amazon and B&N ebook services) would I be noticed.
So, this might be progress, but there are still a lot of holes in their methodology, making this a limited step forward.
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