An example of such a structural reason comes from Andrew Odlyzko: Nuclear Physics B overtook Phys Rev D by lowering author page charges (while jacking up prices). Result: authors sent their best papers their, but prices dramatically rose.
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Part of the reason for the systemic difference is that the market actually works in other areas. That means that capital is available to support innovation. The market is so horrid in science that arXiv - which generates billions (ultimately trillions, IMO) in consumer surplus -
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is barely able to support itself. This is insane (and reminds me of the situation with SSL and the Heartbleed bug).
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(I'm using the term consumer surplus rather loosely, but presume the point is clear: the arXiv deserves to be credited with a huge long-term increase in social welfare, 10^3 or more times its operating budget.)
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